# HG changeset patch # User biomonika # Date 1409869459 14400 # Node ID 05c27700e5caaff920f42407c4495b49afeebeb9 initial commit diff -r 000000000000 -r 05c27700e5ca A.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/A.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,242 @@ +#!/bin/bash +set -e; +email_address_of_user=$1; +echo "email: " $email_address_of_user; + +newline () { + echo -e "\n---"; +} +#variables +mother_contigs=`cat references/reference_contig_names | wc -l`; +echo -e "A variant"; newline; dir=A/; mkdir -p $dir; + +#DAUGHTER PREPARE FILES + + grep -E '#|AF1=0.' vcf/aln_0.85_daughter.vcf | cut -f1 | uniq >${dir}daughter_on_mother_one_allele_heterozygous_ids.vcf + perl -MFile::Slurp -ne 'BEGIN{@a{split(/\s/,read_file("A/daughter_on_mother_one_allele_heterozygous_ids.vcf"))}=()}; $b=$_; @data = split(/\s/, $b); $res=$data[0]; print if exists $a{$res}' vcf/aln_0.85_daughter.vcf | sort | uniq | sed '/#/d' >${dir}daughter_on_mother_heterozygous.vcf + + #be aware that if there are more snps, one with allele frequency '0.' is enough for the whole contig to be in contig_pos_ref_heterozygous + sed '/#/d' ${dir}daughter_on_mother_heterozygous.vcf | perl -pe 's/(comp\S+)\t(\d+)\t\.\t(\S+)\t(\S+).+/$1\t$2\t$3\t$4/' | sort >${dir}contig_pos_ref_alt_daughter_heterozygous + cut -f 1 ${dir}contig_pos_ref_alt_daughter_heterozygous | sort | uniq >${dir}contigs_where_daughter_heterozygous + + sed '/#/d' vcf/aln_0.85_daughter.vcf | perl -pe 's/(comp\S+)\t(\d+)\t\.\t(\S+)\t(\S+).+/$1\t$2\t$3\t$4/' | sort >${dir}contig_pos_ref_alt_daughter + +#FATHER PREPARE FILES + + sed '/#/d' vcf/aln_0.85_father.vcf | perl -pe 's/(comp\S+)\t(\d+)\t\.\t(\S+)\t(\S+).+/$1\t$2\t$3\t$4/' | sort >${dir}contig_pos_ref_alt_father + +#SON PREPARE FILES + + sed '/#/d' vcf/aln_0.85_son.vcf | perl -pe 's/(comp\S+)\t(\d+)\t\.\t(\S+)\t(\S+).+/$1\t$2\t$3\t$4/' | sort >${dir}contig_pos_ref_alt_son + + +echo -e "Step 0 of 3.\nMother must be homozygote."; + sed '/#/d' vcf/aln_0.85_mother.vcf | cut -f1 | sort | uniq >${dir}contigs_where_mother_differs_from_mother; + differing=`cat ${dir}contigs_where_mother_differs_from_mother | wc -l`; + + perl -MFile::Slurp -ne 'BEGIN{@a{split(/\s/,read_file("A/contigs_where_mother_differs_from_mother"))}=()}; $b=$_; @data = split(/\s/, $b); $res=$data[0]; print if !exists $a{$res}' references/reference_contig_names | sort | uniq >${dir}contigs_where_mother_same_as_mother_unchecked + + #check whether mother really does not contain any father variants + wrong_hits=0; + cat ${dir}contigs_where_mother_same_as_mother_unchecked | (while read line; do + contig_check=`./scripts/test.sh ${line} 4 ${dir}contig_pos_ref_alt_father bam/aln_cleaned_sorted_deduplicated_mother.bam A` + if [[ $contig_check -gt 0 ]]; then + echo "contig: " ${line} "contig_check:" $contig_check >>kontrola; + echo "DID NOT PASS "${line}; + wrong_hits=`expr $wrong_hits + 1` + else + #echo "0K"; + echo ${line} >>${dir}contigs_where_mother_same_as_mother + fi + done; + echo "There is this number of wrong variants: "$wrong_hits; + ) + + same=`cat ${dir}contigs_where_mother_same_as_mother | wc -l`; + echo -e "Number of contigs, where mother differs: $differing."; + echo -e "NUMBER of contigs AFTER just this filter: $same/$mother_contigs"; + + newline; + +echo -e "Step 1 of 3.\nSons must be same as mother."; + #First we have to get rid of the intersection with father, possible Y variants do not matter in the calculation + comm -12 ${dir}contig_pos_ref_alt_son ${dir}contig_pos_ref_alt_father | sort | uniq >${dir}possible_Yvariants + cut -f 1 ${dir}possible_Yvariants | sort | uniq >${dir}contigs_with_possible_Yvariants + + #if these possible_Yvariants are in the daughter, they are not Y variants + comm -12 ${dir}contig_pos_ref_alt_daughter ${dir}possible_Yvariants | sort | uniq >${dir}NOT_Yvariants + cut -f 1 ${dir}NOT_Yvariants | sort | uniq >${dir}contigs_with_NOT_Yvariants + + perl -MFile::Slurp -ne 'BEGIN{@a{split(/\s/,read_file("A/contigs_with_NOT_Yvariants"))}=()}; $b=$_; @data = split(/\s/, $b); $res=$data[0]; print if !exists $a{$res}' ${dir}contigs_with_possible_Yvariants | sort | uniq >${dir}contigs_with_Yvariants + + #contig_pos_ref_alt_Yvariants_confirmed; we deplet just those contigs that contain Y variants and then decide if sons are same as mother + +cat ${dir}contigs_with_Yvariants | (while read line; do + grep ${line} ${dir}contig_pos_ref_alt_father | sort >>${dir}contig_pos_ref_alt_Yvariants_confirmed_pro +done; +) + cat ${dir}contig_pos_ref_alt_Yvariants_confirmed_pro | sort >${dir}contig_pos_ref_alt_Yvariants_confirmed; + + comm -23 ${dir}contig_pos_ref_alt_son ${dir}contig_pos_ref_alt_Yvariants_confirmed | cut -f 1 | sort | uniq >${dir}contigs_where_sons_variation_not_caused_by_father + #rm ${dir}contig_pos_ref_alt_Yvariants_confirmed_pro; + + perl -MFile::Slurp -ne 'BEGIN{@a{split(/\s/,read_file("A/contigs_where_sons_variation_not_caused_by_father"))}=()}; $b=$_; @data = split(/\s/, $b); $res=$data[0]; print if !exists $a{$res}' references/reference_contig_names | sort | uniq >${dir}contigs_where_sons_same_as_mother + + same=`cat ${dir}contigs_where_sons_same_as_mother | wc -l`; + echo -e "Number of contigs, where sons differ: $differing."; + echo -e "NUMBER of contigs AFTER just this filter: $same/$mother_contigs"; + + + newline; +echo -e "Step 2 of 3.\nFather must differ from mother."; + sed '/#/d' vcf/aln_0.85_father.vcf | cut -f1 | sort | uniq >${dir}/contigs_where_father_differs_from_mother; + differing=`cat ${dir}contigs_where_father_differs_from_mother | wc -l`; + echo -e "NUMBER of contigs AFTER just this filter: $differing/$mother_contigs"; + + newline; + +echo -e "Step 3 of 3.\nDaughter must have mother and father alleles."; + #we need daughter to have alleles from both parents (AF stands for 'allele frequency') + + #unique lines in first file mean that those are not subsets of father variants - otherwise they would be in common + comm -23 ${dir}contig_pos_ref_alt_daughter_heterozygous ${dir}contig_pos_ref_alt_father | cut -f 1 | sort | uniq >${dir}daughter_NOT_subset_of_father + + perl -MFile::Slurp -ne 'BEGIN{@a{split(/\s/,read_file("A/daughter_NOT_subset_of_father"))}=()}; $b=$_; @data = split(/\s/, $b); $res=$data[0]; print if !exists $a{$res}' ${dir}contigs_where_daughter_heterozygous | sort | uniq >${dir}/contigs_where_daughter_from_parents + + +same=`cat ${dir}contigs_where_daughter_from_parents | wc -l`; + echo -e "NUMBER of contigs AFTER just this filter: $same/$mother_contigs"; + + newline; + +echo -e "Step 4 of 3.\nDaughters and sons can not have any intersection."; + comm -12 ${dir}contig_pos_ref_alt_daughter ${dir}contig_pos_ref_alt_son >${dir}sons_and_daughters_similiar + cut -f 1 ${dir}sons_and_daughters_similiar | sort | uniq >${dir}contigs_where_sons_and_daughters_similiar + + perl -MFile::Slurp -ne 'BEGIN{@a{split(/\s/,read_file("A/contigs_where_sons_and_daughters_similiar"))}=()}; $b=$_; @data = split(/\s/, $b); $res=$data[0]; print if !exists $a{$res}' ${dir}contigs_where_daughter_heterozygous | sort | uniq >${dir}contigs_where_daughters_and_sons_different_pro + + #check whether they are really different (small amount of variants is also wrong) + + echo -e "daughter contains son variants?" + #check whether daughter really does not contain any of son variants + wrong_hits=0; + cat ${dir}contigs_where_daughters_and_sons_different_pro | (while read line; do + contig_check=`./scripts/test.sh ${line} 4 ${dir}contig_pos_ref_alt_daughter bam/aln_cleaned_sorted_deduplicated_son.bam A` + if [[ $contig_check -gt 0 ]]; then + echo "DID NOT PASS "${line}; + echo "daughter contains son variants DID NOT PASS "${line} >>kontrola + wrong_hits=`expr $wrong_hits + 1` + else + #echo "0K"; + echo ${line} >>${dir}contigs_where_daughters_and_sons_different_un1 + fi + done; + echo "There is this number of wrong variants: "$wrong_hits; + ) + + echo -e "son contains daughter variants?" + #check whether son really does not contain any of daughter variants + wrong_hits=0; + cat ${dir}contigs_where_daughters_and_sons_different_pro | (while read line; do + contig_check=`./scripts/test.sh ${line} 4 ${dir}contig_pos_ref_alt_son bam/aln_cleaned_sorted_deduplicated_daughter.bam A` + if [[ $contig_check -gt 0 ]]; then + echo "DID NOT PASS "${line}; + echo "son contains daughter variants DID NOT PASS "${line} >>kontrola + wrong_hits=`expr $wrong_hits + 1` + else + #echo "0K"; + echo ${line} >>${dir}contigs_where_daughters_and_sons_different_un2 + fi + done; + echo "There is this number of wrong variants: "$wrong_hits; + ) + + comm -12 ${dir}contigs_where_daughters_and_sons_different_un1 ${dir}contigs_where_daughters_and_sons_different_un2 | sort >${dir}contigs_where_daughters_and_sons_different_un + + cat ${dir}contigs_where_daughters_and_sons_different_un | sort | uniq >${dir}contigs_where_daughters_and_sons_different; + +#rm ${dir}contigs_where_daughters_and_sons_different_un1 ${dir}contigs_where_daughters_and_sons_different_un2 ${dir}contigs_where_daughters_and_sons_different_un; + + same=`cat ${dir}contigs_where_daughters_and_sons_different | wc -l`; + echo -e "NUMBER of contigs AFTER just this filter: $same/$mother_contigs"; + +echo -e "Calculating intersection of candidate contigs from steps 0-3."; + + comm -12 ${dir}contigs_where_mother_same_as_mother ${dir}contigs_where_sons_same_as_mother | sort >${dir}first_couple; + comm -12 ${dir}contigs_where_father_differs_from_mother ${dir}contigs_where_daughter_from_parents | sort >${dir}second_couple; + comm -12 ${dir}first_couple ${dir}second_couple | sort >${dir}set1 + comm -12 ${dir}contigs_where_daughters_and_sons_different ${dir}set1 | sort >${dir}set2; + +echo -e "Step -1 of 3.\nCoverage must be sufficient."; + touch ${dir}contigs_with_sufficient_coverage; + +cat ${dir}set2 | (while read line; do + + coverage_check1=`./scripts/get_average_contig_coverage.sh 0.75 ${line} bam/aln_cleaned_sorted_deduplicated_mother.bam 2>/dev/null &`; + coverage_check2=`./scripts/get_average_contig_coverage.sh 0.75 ${line} bam/aln_cleaned_sorted_deduplicated_father.bam 2>/dev/null &`; + coverage_check3=`./scripts/get_average_contig_coverage.sh 0.75 ${line} bam/aln_cleaned_sorted_deduplicated_son.bam 2>/dev/null &`; + coverage_check4=`./scripts/get_average_contig_coverage.sh 0.75 ${line} bam/aln_cleaned_sorted_deduplicated_daughter.bam 2>/dev/null &`; + + coverage_check=$(($coverage_check1 + $coverage_check2 + $coverage_check3 + $coverage_check4)) + if [[ $coverage_check -gt 0 ]]; then + echo "LOW COVERAGE "${line}; + else + #echo "0K"; + echo ${line} >>${dir}contigs_with_sufficient_coverage + fi +done; +) + + + cat ${dir}contigs_with_sufficient_coverage | sort >X_results.txt; + #rm ${dir}first_couple; #rm ${dir}second_couple; #rm ${dir}set1; #rm ${dir}set2; + + #have we found any genes? + + final_contigs=`cat X_results.txt | wc -l`; + echo -e "$final_contigs contigs found fulfilling criteria."; + + + if [ $final_contigs -gt 0 ]; then + #we found SOME genes + + #prepare files for sorting into the categories + samtools view -bq 1 bam/aln_cleaned_sorted_deduplicated_mother.bam >${dir}high_score_mother.bam & + samtools view -bq 1 bam/aln_cleaned_sorted_deduplicated_father.bam >${dir}high_score_father.bam & + samtools view -bq 1 bam/aln_cleaned_sorted_deduplicated_daughter.bam >${dir}high_score_daughter.bam & + samtools view -bq 1 bam/aln_cleaned_sorted_deduplicated_son.bam >${dir}high_score_son.bam & + wait; + + samtools index ${dir}high_score_mother.bam & + samtools index ${dir}high_score_father.bam & + samtools index ${dir}high_score_daughter.bam & + samtools index ${dir}high_score_son.bam & + wait; + + #get sequences based on ids + perl scripts/get_sequences_based_on_ids.pl references/reference.fasta X_results.txt >X_results_sequences.txt; + + get_results_in_bam_file () + { + for ARG in "$@"; + do + ./scripts/createBamFromResults.sh X_results.txt bam/aln_cleaned_sorted_deduplicated_${ARG}.bam bam/${ARG}.bam; + 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b/LINKYX_identify_X_linked_SNPs.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,311 @@ +#!/bin/bash + +#LINKYX_PATH set during toolshed installation + +results=$1 #X-linked candidates written here + +reference=${2} +mother_bam=${3} +mother_vcf=${4} +father_bam=${5} +father_vcf=${6} +daughter_bam=${7} +daughter_vcf=${8} +son_bam=${9} +son_vcf=${10} + +results_fasta=${11} + +file_exists () + { + for ARG in "$@"; + do + if [ ! -f ${ARG} ]; then + echo "File $ARG not found"; + fi + done; + } + +#index bam files + +index_bam_file () + { + for ARG in "$@"; + do + bam_file_index=${ARG}".bai" + if [ -e $bam_file_index ]; + then + echo "Index already exists. Not being created again."; + else + samtools index ${ARG} & + fi + done; + } + +idxstats_bam_file () + { + #get statistics about mapped and unmapped reads for every contig + echo "Idxstats" $1 $2; + stat_name=statistics/stat_${2}; + samtools idxstats $1 >$stat_name #statistics for bam files mapping on male reference + + #with MAPQ>0 + samtools view -bq 1 $1 >statistics/high_score_${2}.bam + samtools index statistics/high_score_${2}.bam + + stat_high_name=statistics/stat_${2}_high + samtools idxstats statistics/high_score_${2}.bam >$stat_high_name #statistics for bam files mapping on male reference with MAPQ>0 + } + + +file_exists $testing $results $reference $mother_bam $mother_vcf $father_bam $father_vcf $daughter_bam $daughter_vcf $son_bam $son_vcf #check if all input files are present +index_bam_file $mother_bam $father_bam $daughter_bam $son_bam #index bam files + +#retrieve statistics +mkdir -p statistics; +idxstats_bam_file $mother_bam mother +idxstats_bam_file $father_bam father +idxstats_bam_file $daughter_bam daughter +idxstats_bam_file $son_bam son + +newline () { + echo -e "\n---"; +} + +#variables + +dir="A/"; +echo -e "A variant"; newline; mkdir -p A references bam; + +grep ">" $reference | sed 's/>//g' >references/reference_contig_names +mother_contigs=`cat references/reference_contig_names | wc -l`; + +#DAUGHTER PREPARE FILES + + grep -E '#|AF1=0.' $daughter_vcf | cut -f1 | uniq >${dir}daughter_on_mother_one_allele_heterozygous_ids.vcf + perl -MFile::Slurp -ne 'BEGIN{@a{split(/\s/,read_file("A/daughter_on_mother_one_allele_heterozygous_ids.vcf"))}=()}; $b=$_; @data = split(/\s/, $b); $res=$data[0]; print if exists $a{$res}' $daughter_vcf | sort | uniq | sed '/#/d' >${dir}daughter_on_mother_heterozygous.vcf + + #be aware that if there are more snps, one with allele frequency '0.' is enough for the whole contig to be in contig_pos_ref_heterozygous + sed '/#/d' ${dir}daughter_on_mother_heterozygous.vcf | perl -pe 's/(comp\S+)\t(\d+)\t\.\t(\S+)\t(\S+).+/$1\t$2\t$3\t$4/' | sort >${dir}contig_pos_ref_alt_daughter_heterozygous + cut -f 1 ${dir}contig_pos_ref_alt_daughter_heterozygous | sort | uniq >${dir}contigs_where_daughter_heterozygous + + sed '/#/d' $daughter_vcf | perl -pe 's/(comp\S+)\t(\d+)\t\.\t(\S+)\t(\S+).+/$1\t$2\t$3\t$4/' | sort >${dir}contig_pos_ref_alt_daughter + +#FATHER PREPARE FILES + + sed '/#/d' $father_vcf | perl -pe 's/(comp\S+)\t(\d+)\t\.\t(\S+)\t(\S+).+/$1\t$2\t$3\t$4/' | sort >${dir}contig_pos_ref_alt_father + +#SON PREPARE FILES + + sed '/#/d' $son_vcf | perl -pe 's/(comp\S+)\t(\d+)\t\.\t(\S+)\t(\S+).+/$1\t$2\t$3\t$4/' | sort >${dir}contig_pos_ref_alt_son + + +echo -e "Step 0 of 3.\nMother must be homozygote."; + sed '/#/d' $mother_vcf | cut -f1 | sort | uniq >${dir}contigs_where_mother_differs_from_mother; + differing=`cat ${dir}contigs_where_mother_differs_from_mother | wc -l`; + + perl -MFile::Slurp -ne 'BEGIN{@a{split(/\s/,read_file("A/contigs_where_mother_differs_from_mother"))}=()}; $b=$_; @data = split(/\s/, $b); $res=$data[0]; print if !exists $a{$res}' references/reference_contig_names | sort | uniq >${dir}contigs_where_mother_same_as_mother_unchecked + + #check whether mother really does not contain any father variants + wrong_hits=0; + cat ${dir}contigs_where_mother_same_as_mother_unchecked | (while read line; do + contig_check=`bash ${LINKYX_PATH}/scripts/test.sh ${line} 4 ${dir}contig_pos_ref_alt_father $mother_bam A` + if [[ $contig_check -gt 0 ]]; then + echo "contig: " ${line} "contig_check:" $contig_check >>kontrola; + echo "DID NOT PASS "${line}; + wrong_hits=`expr $wrong_hits + 1` + else + #echo "0K"; + echo ${line} >>${dir}contigs_where_mother_same_as_mother + fi + done; + echo "There is this number of wrong variants: "$wrong_hits; + ) + + same=`cat ${dir}contigs_where_mother_same_as_mother | wc -l`; + echo -e "Number of contigs, where mother differs: $differing."; + echo -e "NUMBER of contigs AFTER just this filter: $same/$mother_contigs"; + +newline; + +echo -e "Step 1 of 3.\nSons must be same as mother."; + #First we have to get rid of the intersection with father, possible Y variants do not matter in the calculation + comm -12 ${dir}contig_pos_ref_alt_son ${dir}contig_pos_ref_alt_father | sort | uniq >${dir}possible_Yvariants + cut -f 1 ${dir}possible_Yvariants | sort | uniq >${dir}contigs_with_possible_Yvariants + + #if these possible_Yvariants are in the daughter, they are not Y variants + comm -12 ${dir}contig_pos_ref_alt_daughter ${dir}possible_Yvariants | sort | uniq >${dir}NOT_Yvariants + cut -f 1 ${dir}NOT_Yvariants | sort | uniq >${dir}contigs_with_NOT_Yvariants + + perl -MFile::Slurp -ne 'BEGIN{@a{split(/\s/,read_file("A/contigs_with_NOT_Yvariants"))}=()}; $b=$_; @data = split(/\s/, $b); $res=$data[0]; print if !exists $a{$res}' ${dir}contigs_with_possible_Yvariants | sort | uniq >${dir}contigs_with_Yvariants + + #contig_pos_ref_alt_Yvariants_confirmed; we deplet just those contigs that contain Y variants and then decide if sons are same as mother + + touch ${dir}contig_pos_ref_alt_Yvariants_confirmed_pro #todo - needs to be created? +cat ${dir}contigs_with_Yvariants | (while read line; do + grep ${line} ${dir}contig_pos_ref_alt_father | sort >>${dir}contig_pos_ref_alt_Yvariants_confirmed_pro +done; +) + cat ${dir}contig_pos_ref_alt_Yvariants_confirmed_pro | sort >${dir}contig_pos_ref_alt_Yvariants_confirmed; + + comm -23 ${dir}contig_pos_ref_alt_son ${dir}contig_pos_ref_alt_Yvariants_confirmed | cut -f 1 | sort | uniq >${dir}contigs_where_sons_variation_not_caused_by_father + #rm ${dir}contig_pos_ref_alt_Yvariants_confirmed_pro; + + perl -MFile::Slurp -ne 'BEGIN{@a{split(/\s/,read_file("A/contigs_where_sons_variation_not_caused_by_father"))}=()}; $b=$_; @data = split(/\s/, $b); $res=$data[0]; print if !exists $a{$res}' references/reference_contig_names | sort | uniq >${dir}contigs_where_sons_same_as_mother + + same=`cat ${dir}contigs_where_sons_same_as_mother | wc -l`; + echo -e "Number of contigs, where sons differ: $differing."; + echo -e "NUMBER of contigs AFTER just this filter: $same/$mother_contigs"; + + + newline; +echo -e "Step 2 of 3.\nFather must differ from mother."; + sed '/#/d' $father_vcf | cut -f1 | sort | uniq >${dir}/contigs_where_father_differs_from_mother; + differing=`cat ${dir}contigs_where_father_differs_from_mother | wc -l`; + echo -e "NUMBER of contigs AFTER just this filter: $differing/$mother_contigs"; + + newline; + +echo -e "Step 3 of 3.\nDaughter must have mother and father alleles."; + #we need daughter to have alleles from both parents (AF stands for 'allele frequency') + + #unique lines in first file mean that those are not subsets of father variants - otherwise they would be in common + comm -23 ${dir}contig_pos_ref_alt_daughter_heterozygous ${dir}contig_pos_ref_alt_father | cut -f 1 | sort | uniq >${dir}daughter_NOT_subset_of_father + + perl -MFile::Slurp -ne 'BEGIN{@a{split(/\s/,read_file("A/daughter_NOT_subset_of_father"))}=()}; $b=$_; @data = split(/\s/, $b); $res=$data[0]; print if !exists $a{$res}' ${dir}contigs_where_daughter_heterozygous | sort | uniq >${dir}/contigs_where_daughter_from_parents + + +same=`cat ${dir}contigs_where_daughter_from_parents | wc -l`; + echo -e "NUMBER of contigs AFTER just this filter: $same/$mother_contigs"; + + newline; + +echo -e "Step 4 of 3.\nDaughters and sons can not have any intersection."; + comm -12 ${dir}contig_pos_ref_alt_daughter ${dir}contig_pos_ref_alt_son >${dir}sons_and_daughters_similiar + cut -f 1 ${dir}sons_and_daughters_similiar | sort | uniq >${dir}contigs_where_sons_and_daughters_similiar + + perl -MFile::Slurp -ne 'BEGIN{@a{split(/\s/,read_file("A/contigs_where_sons_and_daughters_similiar"))}=()}; $b=$_; @data = split(/\s/, $b); $res=$data[0]; print if !exists $a{$res}' ${dir}contigs_where_daughter_heterozygous | sort | uniq >${dir}contigs_where_daughters_and_sons_different_pro + + #check whether they are really different (small amount of variants is also wrong) + + echo -e "daughter contains son variants?" + #check whether daughter really does not contain any of son variants + wrong_hits=0; + cat ${dir}contigs_where_daughters_and_sons_different_pro | (while read line; do + contig_check=`bash ${LINKYX_PATH}/scripts/test.sh ${line} 4 ${dir}contig_pos_ref_alt_daughter $son_bam A` + if [[ $contig_check -gt 0 ]]; then + echo "DID NOT PASS "${line}; + echo "daughter contains son variants DID NOT PASS "${line} >>kontrola + wrong_hits=`expr $wrong_hits + 1` + else + #echo "0K"; + echo ${line} >>${dir}contigs_where_daughters_and_sons_different_un1 + fi + done; + echo "There is this number of wrong variants: "$wrong_hits; + ) + + echo -e "son contains daughter variants?" + #check whether son really does not contain any of daughter variants + wrong_hits=0; + cat ${dir}contigs_where_daughters_and_sons_different_pro | (while read line; do + contig_check=`bash ${LINKYX_PATH}/scripts/test.sh ${line} 4 ${dir}contig_pos_ref_alt_son $daughter_bam A` + if [[ $contig_check -gt 0 ]]; then + echo "DID NOT PASS "${line}; + echo "son contains daughter variants DID NOT PASS "${line} >>kontrola + wrong_hits=`expr $wrong_hits + 1` + else + #echo "0K"; + echo ${line} >>${dir}contigs_where_daughters_and_sons_different_un2 + fi + done; + echo "There is this number of wrong variants: "$wrong_hits; + ) + + comm -12 ${dir}contigs_where_daughters_and_sons_different_un1 ${dir}contigs_where_daughters_and_sons_different_un2 | sort >${dir}contigs_where_daughters_and_sons_different_un + + cat ${dir}contigs_where_daughters_and_sons_different_un | sort | uniq >${dir}contigs_where_daughters_and_sons_different; + +#rm ${dir}contigs_where_daughters_and_sons_different_un1 ${dir}contigs_where_daughters_and_sons_different_un2 ${dir}contigs_where_daughters_and_sons_different_un; + + same=`cat ${dir}contigs_where_daughters_and_sons_different | wc -l`; + echo -e "NUMBER of contigs AFTER just this filter: $same/$mother_contigs"; + + echo -e "Calculating intersection of candidate contigs from steps 0-3."; + + comm -12 ${dir}contigs_where_mother_same_as_mother ${dir}contigs_where_sons_same_as_mother | sort >${dir}first_couple; + comm -12 ${dir}contigs_where_father_differs_from_mother ${dir}contigs_where_daughter_from_parents | sort >${dir}second_couple; + comm -12 ${dir}first_couple ${dir}second_couple | sort >${dir}set1 + comm -12 ${dir}contigs_where_daughters_and_sons_different ${dir}set1 | sort >${dir}set2; + +cat ${dir}set2 >>results; #todo remove +echo -e "Number of contigs after intersection: " `cat ${dir}set2 | wc -l`; + +echo -e "Step -1 of 3.\nCoverage must be sufficient."; + touch ${dir}contigs_with_sufficient_coverage; + +cat ${dir}set2 | (while read line; do + + coverage_check1=`bash ${LINKYX_PATH}/scripts/get_average_contig_coverage.sh 0.75 ${line} $mother_bam $reference 2>/dev/null &`; + coverage_check2=`bash ${LINKYX_PATH}/scripts/get_average_contig_coverage.sh 0.75 ${line} $father_bam $reference 2>/dev/null &`; + coverage_check3=`bash ${LINKYX_PATH}/scripts/get_average_contig_coverage.sh 0.75 ${line} $son_bam $reference 2>/dev/null &`; + coverage_check4=`bash ${LINKYX_PATH}/scripts/get_average_contig_coverage.sh 0.75 ${line} $daughter_bam $reference 2>/dev/null &`; + + #echo "coverage check: " $coverage_check1 $coverage_check2 $coverage_check3 $coverage_check4 + + coverage_check=$(($coverage_check1 + $coverage_check2 + $coverage_check3 + $coverage_check4)) + if [[ $coverage_check -gt 0 ]]; then + echo "LOW COVERAGE "${line}; + else + echo "COVERAGE 0K"; + echo ${line} >>${dir}contigs_with_sufficient_coverage + fi +done; +) + + cat ${dir}contigs_with_sufficient_coverage | sort >X_results.txt; + +#have we found any genes? + final_contigs=`cat X_results.txt | wc -l`; + echo -e "$final_contigs contigs found fulfilling criteria."; + + if [ $final_contigs -gt 0 ]; then + #we found SOME genes + + #retrieve sequences in fasta + perl ${LINKYX_PATH}/scripts/get_sequences_based_on_ids.pl $reference X_results.txt >X_results_sequences.fasta; + #sort sequences + perl ${LINKYX_PATH}/scripts/sorting.pl A/ $reference ${LINKYX_PATH} >>$results + + get_results_in_bam_file () + { + #candidates full_bam_file candidates_bam_file + cat X_results.txt | xargs samtools view -F 4 -b $1 > $2; + samtools index $2 + } + + get_results_in_bam_file $mother_bam ${12} #argument for output bam file mother + get_results_in_bam_file $father_bam ${13} #argument for output bam file father + get_results_in_bam_file $daughter_bam ${14} #argument for output bam file daughter + get_results_in_bam_file $son_bam ${15} #argument for output bam file son + wait; + + #send BAM files with corresponding contigs + #mutt -s "LINKYX: Results of computation for X-linked genes" $email_address_of_user -a bam/mother.bam -a bam/mother.bam.bai -a bam/father.bam -a bam/father.bam.bai -a bam/daughter.bam -a bam/daughter.bam.bai -a bam/son.bam -a bam/son.bam.bai < messages_to_user/message_results_sentBamX; + + else + #we found NO genes + echo "No sequences found." >X_results.txt; + echo "No sequences found." >X_results_sequences.fasta; + fi + + newline; +echo -e "Writing output to X_results.txt"; +echo -e "Total number of found X-linked genes: $final_contigs"; + +#TEST OUTPUT + cat X_results.txt >>$results + cat X_results_sequences.fasta >>$results_fasta + ls -lah */* >>$results + + diff -r 000000000000 -r 05c27700e5ca LINKYX_identify_X_linked_SNPs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LINKYX_identify_X_linked_SNPs.xml Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,39 @@ + + Identify X linked contigs from cross + + LINKYX_PATH + SAMTOOLS + samtools + + LINKYX_identify_X_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $input6 $input7 $input8 $input9 $output1 $output2 $output3 $output4 $output5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool identifies X linked contigs from cross (represented as 4 VCF files). + + + \ No newline at end of file diff -r 000000000000 -r 05c27700e5ca LINKYX_identify_Y_linked_SNPs.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LINKYX_identify_Y_linked_SNPs.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,114 @@ +#!/bin/bash + +#LINKYX_PATH set during toolshed installation + +results=$1 #X-linked candidates written here + +reference=${2} +mother_male_bam=${3} +father_male_bam=${4} +daughter_male_bam=${5} +son_male_bam=${6} + +results_fasta=${7} + +mkdir -p Y references; dir="Y/"; +grep ">" $reference | sed 's/>//g' >references/male_contig_names + +file_exists () + { + for ARG in "$@"; + do + if [ ! -f ${ARG} ]; then + echo "File $ARG not found"; + fi + done; + } + +#index bam files + +index_bam_file () + { + for ARG in "$@"; + do + bam_file_index=${ARG}".bai" + if [ -e $bam_file_index ]; + then + echo "Index already exists. Not being created again."; + else + samtools index ${ARG}; + fi + done; + } + +#get statistics about mapped and unmapped reads for every contig + +idxstats_bam_file () + { + #get statistics about mapped and unmapped reads for every contig + echo "Idxstats" $1 $2; + stat_male_name=statistics/stat_male_${2}; + samtools idxstats $1 >$stat_male_name #statistics for bam files mapping on male reference + + #with MAPQ>0 + samtools view -bq 1 $1 >statistics/high_score_male_${2}.bam + samtools index statistics/high_score_male_${2}.bam + + stat_male_high_name=statistics/stat_male_${2}_high + samtools idxstats statistics/high_score_male_${2}.bam >$stat_male_high_name #statistics for bam files mapping on male reference with MAPQ>0 + } + +echo "Checking existence of input bam files." +file_exists $mother_male_bam $father_male_bam $son_male_bam $daughter_male_bam +index_bam_file $mother_male_bam $father_male_bam $son_male_bam $daughter_male_bam + +#retrieve statistics +mkdir -p statistics; +idxstats_bam_file $mother_male_bam mother +idxstats_bam_file $father_male_bam father +idxstats_bam_file $daughter_male_bam daughter +idxstats_bam_file $son_male_bam son + +#read statistics +reads_number_mother=`awk '{read_number+=($3+$4)} END {print read_number}' statistics/stat_male_mother`; +reads_number_father=`awk '{read_number+=($3+$4)} END {print read_number}' statistics/stat_male_father`; +reads_number_daughter=`awk '{read_number+=($3+$4)} END {print read_number}' statistics/stat_male_daughter`; +reads_number_son=`awk '{read_number+=($3+$4)} END {print read_number}' statistics/stat_male_son`; + +echo "Reads numbers: " $reads_number_mother $reads_number_father $reads_number_daughter $reads_number_son + +#filter contigs, which are candidate Y genes - very divergent from their X counterparts +perl ${LINKYX_PATH}/scripts/filter_diverged_Y_contigs.pl $reads_number_mother $reads_number_father $reads_number_daughter $reads_number_son $reference ${LINKYX_PATH} >Y_results.txt; + +echo "Y_results: " >>$results + +final_contigs=`cat Y_list | wc -l` +#have we found any genes? + +if [ $final_contigs -gt 0 ]; then + #we found SOME genes + #retrieve sequences in fasta + perl ${LINKYX_PATH}/scripts/get_sequences_based_on_ids.pl $reference Y_list >Y_results_sequences.fasta; + + get_results_in_bam_file () + { + #candidates full_bam_file candidates_bam_file + cat Y_list | xargs samtools view -F 4 -b $1 > $2; + samtools index $2 + } + + get_results_in_bam_file $mother_male_bam ${8} #argument for output bam file mother + get_results_in_bam_file $father_male_bam ${9} #argument for output bam file father + get_results_in_bam_file $daughter_male_bam ${10} #argument for output bam file daughter + get_results_in_bam_file $son_male_bam ${11} #argument for output bam file son + wait; +else + #we found NO genes + echo "No sequences found." >Y_results.txt; + echo "No sequences found." >Y_results_sequences.fasta; + fi + +#output results to Galaxy + cat Y_results.txt >>$results + cat Y_results_sequences.fasta >>$results_fasta + ls -lah */* >>$results diff -r 000000000000 -r 05c27700e5ca LINKYX_identify_Y_linked_SNPs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LINKYX_identify_Y_linked_SNPs.xml Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,34 @@ + + Identify Y linked contigs from cross + + LINKYX_PATH + SAMTOOLS + samtools + + LINKYX_identify_Y_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $output1 $output2 $output3 $output4 $output5 + + + + + + + + + + + + + + + + + + + + + + + This tool identifies Y linked contigs from cross (represented as 4 bam files mapped on male reference). + + + \ No newline at end of file diff -r 000000000000 -r 05c27700e5ca LINKYX_mpileup_wrapper.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LINKYX_mpileup_wrapper.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,12 @@ +#!/bin/bash +results=$1; +bam_file=$2; +reference=$3; + +sorted_bam=${bam_file}_sorted + +#LINKYX_PATH set during toolshed installation + +samtools mpileup -uf $reference $bam_file 2>log.txt | bcftools view -p 0.85 -cgv - 2>log.txt >$results + +#samtools mpileup -uf $reference $2 2>log.txt | bcftools view -p 0.85 -cgv - 2>>log.txt| vcfutils.pl varFilter >$results 2>>log.txt \ No newline at end of file diff -r 000000000000 -r 05c27700e5ca LINKYX_mpileup_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LINKYX_mpileup_wrapper.xml Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,22 @@ + + Run mpileup with LINKYX-specific parameters + LINKYX_mpileup_wrapper.sh $output $input1 $input2 + + + + + + + + + + + + + + + + This tool tests if primers are present in gorilla female or on human Y or chimp Y chromosome. + + + \ No newline at end of file diff -r 000000000000 -r 05c27700e5ca README.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,14 @@ +LinkYX + +Fully automated pipeline for detection of sex linked genes using RNA-Seq data +bitbucket.org/biomonika/linkyx + +Please install following dependencies from toolshed: +toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4 +toolshed.g2.bx.psu.edu/repos/bhaas/trinityrnaseq/trinityrnaseq/0.0.1 +toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 +toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4 +toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2 +toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0 + +If you have any questions, please use following email address: biomonika@psu.edu \ No newline at end of file diff -r 000000000000 -r 05c27700e5ca Y.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Y.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,32 @@ +#!/bin/bash +set -e; +email_address_of_user=$1; +echo "email: " $email_address_of_user; + +echo "Calculation of Y-linked genes started." +./scripts/prepare_statistics.sh; +echo "Statistics done"; + +#filter contigs, which are candidate Y genes - very divergent from their X counterparts +perl scripts/filter_diverged_Y_contigs.pl scripts/statistics/stat_mother scripts/statistics/stat_father scripts/statistics/stat_daughter scripts/statistics/stat_son >Y_results.txt; +perl scripts/get_sequences_based_on_ids.pl references/reference_male.fasta Y_list >Y_results_sequences.txt; + +if [[ -s Y_list ]] ; then + get_results_in_bam_file () + { + for ARG in "$@"; + do + ./scripts/createBamFromResults.sh Y_list bam/aln_cleaned_sorted_deduplicated_${ARG}_male.bam bam/${ARG}_male.bam; + samtools index bam/${ARG}_male.bam; + done; + } + + get_results_in_bam_file mother father daughter son; + wait; + #send BAM files with corresponding contigs + mutt -s "LINKYX: Results of computation for Y-linked genes" $email_address_of_user -a bam/mother_male.bam -a bam/mother_male.bam.bai -a bam/father_male.bam -a bam/father_male.bam.bai -a bam/daughter_male.bam -a bam/daughter_male.bam.bai -a bam/son_male.bam -a bam/son_male.bam.bai < messages_to_user/message_results_sentBamY; +else + #we found NO genes + echo "No sequences found." >Y_results.txt; + echo "No sequences found." >Y_results_sequences.txt; +fi \ No newline at end of file diff -r 000000000000 -r 05c27700e5ca demo_files/.DS_Store Binary file demo_files/.DS_Store has changed diff -r 000000000000 -r 05c27700e5ca demo_files/daughter.bam Binary file demo_files/daughter.bam has changed diff -r 000000000000 -r 05c27700e5ca demo_files/daughter.bam.bai Binary file demo_files/daughter.bam.bai has changed diff -r 000000000000 -r 05c27700e5ca demo_files/daughter_1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/demo_files/daughter_1.fastq Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,516 @@ +@HISEQ1:121:C0EP5ACXX:8:1301:12962:135792/1 +AATGGTCTCTCTCCTCTAAAACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGC ++ +HICEGFFGHGHHIIIIGGIJJIGGIIDE@GIIJIJCHGCHIEHIIJJIGDHJJFFEFEFEFBBDDDEACCEEBB=CBDDEDDCACC? +@HISEQ1:121:C0EP5ACXX:8:1105:5390:32380/1 +AAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCC ++ +IJJJJJJJJJJJJIJJJJJJJJJIJJJJJJIIJIJJJJJIJJJJJJJJHIJJJJGGEIHHE?EHFFFFECADCD;ACBCDDDEEACC +@HISEQ1:121:C0EP5ACXX:8:1301:11290:183940/1 +TCCTCTAAAACGCTCTCTCCTCTCTCTACAGTGTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAG ++ +IJJJIIJJJJIIJJIHIJGGGIGIIJIIJGHDHIJJJJJJJJJJJGIJJJHIHIIIIIHGIHFHHFFFFFDCECCDDDDDDDDDDC< +@HISEQ1:121:C0EP5ACXX:8:2207:5683:120579/1 +GTGTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTTGCTCCTCCCCTCTGTGCTTGTTTTC ++ +IIJIIIJIJJJIJJIJJIFGIJJJIJJJIJIIHGJJJIJJIHHHJHIIGJJIJIDGIJIJJEHFGFHFFFFCCCCDDCCDCDDDCD> +@HISEQ1:121:C0EP5ACXX:8:1301:12479:185948/1 +GAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCCCCACAATTTGCAAGGGCANN ++ +JHHIIJJJJJIJJGGGHEDHHGHJFHHIIBFFIIFGIJIFIIJFGHJIIDIDACEEHHFFA=>>B@CDDCDDDDCDDDDDDDCDDDD +@HISEQ1:121:C0EP5ACXX:8:2103:4989:50580/1 +TCTCTCTCCTCTAAAACGCTCTCTCCTCTCTCTACAGTGTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGG ++ +ACGFHHGIIIIGGEHIIACDDDBDBB@9>BDDDCDDDDDCDDE: +@HISEQ1:121:C0EP5ACXX:8:2304:11218:150303/1 +GCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCCCCACN ++ +HIIIJJJJJJJJJJJJIIJJIJJIIIJJBGIJJIIIHIJHICHIFGEHIIJJHH=CEFFAEBEEDD@DCEFDBDDDDD@BBDDDDDD +@HISEQ1:121:C0EP5ACXX:8:2102:13316:62111/1 +AGCTTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGT ++ +GGBHEIEEEDHI>GHGIJIHIIGDBCHEHIJIIJEFEGHGIJIHHHJE>@FHC>CHCCAEA??BD?CEDEEECCCDDDCDCDDCDA5 +@HISEQ1:121:C0EP5ACXX:8:1106:3218:101980/1 +TCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTG ++ +IJIJJJJJJIJGHIJIIGGGIJJJIIJJJJJJJJJJJJJJJGBGGGHGJIJJJGHIJJFCHEHFFFFEBEEEEEDDDDDDDDDDAC: +@HISEQ1:121:C0EP5ACXX:8:1201:18503:100349/1 +AAAACGCTCTCTCCTCTCTCTACAGTGTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTT ++ +HICGI::BBBCCC@@C@C??=9?C +@HISEQ1:121:C0EP5ACXX:8:1204:4243:118195/1 +CAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAAAATCGAAAGAGAGGCN ++ +:?ADABCB>?@@3@DDGEE>EDFFGFF=BBB;F?;FFBE9;CEFD=@DCC?6=?5:AAAB?3,20(258399??AB?A<993<<@?B +@HISEQ1:121:C0EP5ACXX:8:1106:18868:150736/1 +TCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAAAATCGNNNNNNN ++ +IGGEIGIICHHEHFGBHF>>@CDDDDDDDDC: +@HISEQ1:121:C0EP5ACXX:8:2104:7464:97678/1 +GAGATTCCGGTGAGAGCAGCCTTCAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATC ++ +BGIGGIIIII)?EEGCHIIBHEIIIHHIIHEGGCHIIEGIIIGIIGEGE6AE;?ECEEBBBBA?8??@B@BBB??@@8??BCBBBB> +@HISEQ1:121:C0EP5ACXX:8:1106:9192:29781/1 +TCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTT ++ +IIJJIJJIIJJJIJIIJGHJIJIGJIJJJJJJJJJIIIIJJJJJJIJJJJJJIJJJIIJJHHHHFFFDFFEACECEDDDDDDDDDDA +@HISEQ1:121:C0EP5ACXX:8:2302:12102:76322/1 +CAAGTGAAGAGATTCCGGTGAGAGCAGCCTTCAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAG ++ +JJJJHIJJJJJJJJJJJJDHIJJJIJJJJJJJJJJJIJJJJJJJJJJJJJJJJJHHHFFDDABDDDDDDDDDDDDDDDDDBBDDDDD +@HISEQ1:121:C0EP5ACXX:8:1202:10923:67043/1 +ACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCC ++ +JJJJJGGIJJJIEHIGHGIIEHIIIGIJGIJJJJJJIHIJJICFHGIGHHJIGICHIHGHHGEEEDEF@C96;@CD +@HISEQ1:121:C0EP5ACXX:8:2303:8797:124341/1 +CCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCG ++ +JJJJJJIIGHJJIEHIJGIJJIJIJJJI@FHGIJFGIJJHGIFGGGGIJCHIIIHIJJJHHHHHFFFFDFCCCCD?>==CCDDDDDD +@HISEQ1:121:C0EP5ACXX:8:1304:8551:182744/1 +CCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCG ++ +EBFHCAGGIGH@AHECBCGECG?FHIGIADHIIEGGDFA?BED=@28)=@@@EGG@D@@EE:?.7);?BDC@C=A@=@?(5=/;@@ +@HISEQ1:121:C0EP5ACXX:8:2205:17966:149411/1 +GAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTTCAATCCATCTCCAATCACCATTCGCN ++ +JIJJJJJIJJJJFHGIJJJJJJJJIJJIJJIIJJFHJJJIJJJJJJJJFHIJJHHHHFFFEFEDEEEEDDDDD@CDDCDDDDDDCD< +@HISEQ1:121:C0EP5ACXX:8:2204:7913:47072/1 +CTCTAAAACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCT ++ +GGIIIJJGEBEGB@CCBDDDDDCDDDAB=B +@HISEQ1:121:C0EP5ACXX:8:1206:14809:89750/1 +TCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTTCAATCAATCTCCAATCAC ++ +GGEICEHIIIGIICHIJHGGEFIEGEGGGGGHIJJFEGIJJDCGBBGEICGGHIJAEFFFFDDEEAEECCDEDDDCDDC@C?CDDD +@HISEQ1:121:C0EP5ACXX:8:1107:8614:188228/1 +GGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTTCAATCCATCTCCNN ++ +IJIJJIGIJJJGIDIIJJIIFGIJGIJIJJHHGFEHGFFFFFDDDD@CDDDCDDDDDEDB?F7F9:@B<;@;77/=))).)==;C9E7)7;2=?@(;;3;;>((,:;;>@@<7@@::3:C +@HISEQ1:121:C0EP5ACXX:8:1302:20544:36891/1 +GCTCTCTCCTCTCTCTACAGTGTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTTGCTCC ++ +IIIJJJJJJJJGIGIJJJIJGHBGIIGHGIIGJJJJIJJJJJJIIJIIJIJEHJJIIJJEEHHHFFDDFEEEEDADDDDDDDCDDD +@HISEQ1:121:C0EP5ACXX:8:1201:13712:106244/1 +TCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTN ++ +IJJJJJJJJJJJIIIJIJIJJFHIIIFIGIHIGIIIJIIIIJJIJIJIIHHHHGFDDCEDDEDDDDDDDDDCDCDDDEEDC@CCCD@ +@HISEQ1:121:C0EP5ACXX:8:1205:1987:169105/1 +TTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTC ++ +JJIIIHIIGJIJJJJJJJJJJJHIJIJJIIGGHIIGIFHIIJJJJIJJJIIEHGGHIIIHHHHHF@DEFCDCEEDBD?B?CCDBDDC +@HISEQ1:121:C0EP5ACXX:8:1304:10703:43081/1 +CTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACN ++ +JJJJGIJJJIIJJJHIIGHGHIJJJIIIJJJJJIGIJJJJJJHHGIHII9C?C9?FBDFB<)?B:BG)09D?8BFF<=8B<7=@@FDEC;@A7?;??C;BD);?8998,'5@A>>BB +@HISEQ1:121:C0EP5ACXX:8:2202:11034:3947/1 +CTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACN ++ +JJJJJJJJGJJJJIGHIEFHHHJCCHIIJJJJJJJJJJJJJJHIIJIIIJJHIIIHHHFDDDDBDEDDDDDBDCDDDDDDCCCDDDA +@HISEQ1:121:C0EP5ACXX:8:1101:3334:33169/1 +GAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAG ++ +FFG9?CHGGGHHE6F??*??3BGHI>.@FH45@;;:?EAHE>C;7;;(666(;A(-->;@98555:35;@ +@HISEQ1:121:C0EP5ACXX:8:2104:7518:85500/1 +TCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGG ++ +BEC?CAF@EHEEHAFEHE@DG?B?1??9CG?GIGGGHE??DGGGGEGEECGCE;=C==CH?AAE>DCDB5=ACA>?C@CACCCB3@> +@HISEQ1:121:C0EP5ACXX:8:2104:18741:150825/1 +AAAACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGC ++ +JJJIIJJJHGIJJJJJIIJIIIIEHHIIIJIIJJFDHGIJJJJJJJJJIJIJFG@GHIJHHHHHHBDFFFDEECEDDDDD?CDCCDC +@HISEQ1:121:C0EP5ACXX:8:2103:17562:161306/1 +GAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCC ++ +HBEHGFFEAABDHHIFHGGCA?GBB@DCDDCBCC99CCCCCCA44@+>>@C +@HISEQ1:121:C0EP5ACXX:8:2303:4331:138576/1 +CTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTC ++ +IJJJGEHIIJJIJIJIIJJIJJJIJIGIIIJJJJJI@GHJJBHIICHGHIIJJGGIHEEHHFF>CBFFB>ACACD@ACCCDDCDDD= +@HISEQ1:121:C0EP5ACXX:8:1206:16241:142787/1 +TTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCA ++ +HGGGHIIGGIEIIIHCFFIFBHHEIDEHBED;;@:@AACB88;9>A:@ACBDB?CDDEEC?A?@BD@CCCA +@HISEQ1:121:C0EP5ACXX:8:2305:14287:109430/1 +CATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACACTTAACC ++ +IJJJJJIIJJGIIIJJJJJJJJJJJJJJJJJIIGIGIIIHIJJJJIIJJJJHHF9AEEEDDDDDDDDDDDDDDDDDDDDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:2107:12104:180859/1 +GATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGN ++ +GHGBGHDHBFDHECEGGGBBA@FDFAHEBFD@>@3>CD>A=:059?CCCCC38+28?@>ADAB: +@HISEQ1:121:C0EP5ACXX:8:2306:14745:2012/1 +TGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGANNNN ++ +EGIGHGFGIIEFEHDHEIJFGIIIJIGHIJJEIJIICECCEEEFHFDDDB@CECCCCCACDDEDDDDDCACCC@BD@BC +@HISEQ1:121:C0EP5ACXX:8:1107:19971:96047/1 +ACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCC ++ +JJJJJJJJJJJJJJJIJJJJGIHIIIIJIJJJJIJJJJJJJJJIJJJJIHIIFHIIJJJHHHHFHFFFFEECECEDDDDDDDDCDDC +@HISEQ1:121:C0EP5ACXX:8:1102:13754:6046/1 +ACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGT ++ +EDFE@,A?CFEDG9CDEEEACDDDB;;@CC>A;>BB@8<@A>BBB +@HISEQ1:121:C0EP5ACXX:8:1305:16307:34281/1 +ATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGG ++ +JJHIJJJJJJJJIJJJJIJJIIGHJJJJJJJJIJJJJHIJJJJJIJJJJJJJIHFFDEEDDDDDDDCDCDDCDDDB5C@CCDDDDD966@AAA3>5>??:AAAA +@HISEQ1:121:C0EP5ACXX:8:1206:4841:180732/1 +TCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTAT ++ +JJJIHIJJJJJJJIIJJJJIJJJJJIJJJJJIJJJJIIJJGHIJJIIIIIJIIJJJJJJHHGEHFFFFFFEDDDBDACDDBDDD>BA +@HISEQ1:121:C0EP5ACXX:8:2104:5669:156581/1 +TGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCC ++ +CHJHIJJJIIJGGJIJGHJ>FHIJEIJIIIIIIIJJJHGGIIJHIHEHHHEFFFFFFEDCE?CCCDDDDDDB@BCCCDDDEDDDDDD +@HISEQ1:121:C0EP5ACXX:8:1203:5383:144796/1 +CCTCTCTCTACAGTGTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTTGCTCCTCCCCTCT ++ +AEBB?FGHIII@B:EHEGHIHGBHEGGGGIICD9?>?;@B>@@AC((>(;CA5?:5;5 +@HISEQ1:121:C0EP5ACXX:8:1201:18290:177436/1 +CCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGN ++ +JJJJGHIJIIIJJIJJIJJJEHIEHHGGIJJJJJJJJGIHHHHHFFFFFFEEEEEEDCDCDCFDDDDDDCCDDDDD?BB@@@CDDD7 +@HISEQ1:121:C0EP5ACXX:8:1207:3038:16038/1 +CCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGN ++ +FBGGDHIJIJGIIIG>HGIC9?DBFCHHIICDACHDGIIHHHGEDDFEE@CCEEEC>CCAA>@C>A>ACC@@>:?BBBDBBDCDB9< +@HISEQ1:121:C0EP5ACXX:8:1206:16810:160141/1 +AGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTC ++ +GB?DHIIDHGGHJIJFIJJIIIGGHDEE@DEFFECE@C@ACD@CCD@CDDBDDDCDDC@>AACCCDDCCDDDDDBCCCDDDCCA:@ +@HISEQ1:121:C0EP5ACXX:8:2108:13659:50707/1 +AAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTC ++ +IJGIHJBHIDFGIIJEHIJI@HHIIGIJBDAFFGGGGAEHGJ@AEFFEHFDBEFF>CC@CE@>CCCA5@ +@HISEQ1:121:C0EP5ACXX:8:2307:12319:57989/1 +AGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTN ++ +EGGGHHGGHIIJJJJGHI@FHDAHGIGI6@BCCDDDDCDD:ACDC@C@CCDCDDB@DDCCDCC>>?CDDDDDCCDDDDC:>@ACDD> +@HISEQ1:121:C0EP5ACXX:8:1101:8737:95819/1 +GGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCT ++ +JJJIIJJJJJJIJJIJJJIIIJJJJJIJGIIGFHIGHGGIJJJCGEHHHGHFEFFFA?EED@CCDDDDDDBDB>CCDDDDDDDCDD: +@HISEQ1:121:C0EP5ACXX:8:1301:15961:111397/1 +AGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTT ++ +JJJJJJJIJIIJJIGGIGIJJJJIJJHIHHHFCCDDDDDACDDDDDDDDDDDDDDDDDDDDDEDDDDDDDDDDDDDDDDDDEDDDDD +@HISEQ1:121:C0EP5ACXX:8:1302:19521:69299/1 +AACAGAGGCGAGGAACGAAACTCCTTAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTC ++ +IIIEGAGICG>FAHD@@:C3@@: +@HISEQ1:121:C0EP5ACXX:8:1203:3175:113512/1 +AAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTC ++ +IJFIIEHI?EGGHGIJFHIJJEHJIIIEHHEEEEFDDDDDDDDCCCDCCCDDCDCCDDC9BBDDDDC>C>C@CDDCACACCCC@@:> +@HISEQ1:121:C0EP5ACXX:8:1208:3501:162441/1 +TACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGGCCTCCTCTGCTCCC ++ +IIIIIEHH9HIIIIIIBHGEIIII9DHG>BGCA8BGIIIIIHGIIIIIIGIIIIHEEEEA?CBCECCCC@(5??CBBCCCACCCCB +@HISEQ1:121:C0EP5ACXX:8:2102:10284:25123/1 +GCAAATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGAT ++ +FGHHII@IHHIH6?EF@1CDFEE@FHHIHGGIHD=@GEGHEDEEFEFEF?C@DCEDDECCD>ADCC>ACCCCD@@CCCC9ACC>?8@ +@HISEQ1:121:C0EP5ACXX:8:1102:16158:78675/1 +TTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGGCCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATGGATTGAAGGCT ++ +JJJJJJJJJJIIIIIJJJJJJIJHIIJIJJGGIIJJJIJJJJJIJJIJJIHHHHHFEFFDDDDDCCDDEDDCCACCDCDDDDCCDDA +@HISEQ1:121:C0EP5ACXX:8:1203:3978:188625/1 +TGGTTCCCTCCTGGCCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATGGATTG ++ +EHI?EHHG>FGDEC8E9FC3?*:?@DGG>3BDAGGHB)===DCDHIIIJJJJDC>GGGJJJJJGDHHHFHEBDFFFCDEEDDCDCCDDDDDDAC +@HISEQ1:121:C0EP5ACXX:8:1302:7021:199313/1 +TCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAG ++ +JJJJJJJJJJJGIJIIJJIJJJJFIJJJJHHHFFFFFFCEEEEDDDDBDDDDDDDDCCDDDDDDDEDDDBBBDCDEDDDDDDDCCCD +@HISEQ1:121:C0EP5ACXX:8:1306:10437:150125/1 +CTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGNN ++ +JJJJJJIJJGJJIIIJIJJFHIJJIJJJHFHFFFFDEEEEEEDDDDDDDDDDDDDDCDDDDCCDDDEDDDDDDDDDEDDDDDDDDDA +@HISEQ1:121:C0EP5ACXX:8:1202:7387:154438/1 +GCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGNNNNNNNN ++ +JJJJJJJJIJJJJIJIIJJJJJIJJGIJJHHHGHGFFBFDDDDDDDDDDDCDCDDDDDDDECDDBBDDDCDDDDDDDDDDDDDDDD: +@HISEQ1:121:C0EP5ACXX:8:2103:12603:82497/1 +AACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTG ++ +DDDDDDDDDDDDDDDDDDDDDDDDDDBDDDDDDDDDDDDDCDDDDDDDDDDDDCDCDDDDDCDDDDDDEDDD<@DDD@DDDCDDDDD +@HISEQ1:121:C0EP5ACXX:8:2104:11050:81554/1 +TAGGATGGAGCTTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTG ++ +IJJIEGII@FICGGHEGHIIIIJJJIGHG>C@ABDDDBCDACD?@DB +@HISEQ1:121:C0EP5ACXX:8:1102:18712:9225/1 +CAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCANNNN ++ +JJJIIFDGHIJGIIJD6@1ACDB<>BCDDDCDDCCECC>CCDDCC8;ACCEDDD?@C:<;>B +@HISEQ1:121:C0EP5ACXX:8:1108:5820:79317/1 +CCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCANN ++ +JJJJJJJJJJJJJJJJDBDDDDDCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCCDDCCDDCDDDDDDDDDCDCCCC +@HISEQ1:121:C0EP5ACXX:8:1106:6069:149613/1 +GGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAG ++ +IJIIJJJIJJIIJIJIJJIIIJJFIDFHIJIJJJHIJJFGGHJJJJJJJHHHHHFFFFDDBDDDDDDDEDDDCCDDDDDDDDEDDCC +@HISEQ1:121:C0EP5ACXX:8:1106:6337:118237/1 +TTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACACTTAACCCTT ++ +JJJJHIIDHIJJIIJJJJJJJAGIJJJJJJJJJJJJGHJJJGJJJJJJJHE=BEEFEEE;ABDDDDDDDDDCDDDDDDDDDDDDDDA +@HISEQ1:121:C0EP5ACXX:8:1303:16108:108202/1 +CCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATA ++ +ICEFAFGGIIGEDAF?FGI>CC4D>A=B=FC9F@C4@ +@HISEQ1:121:C0EP5ACXX:8:1107:11975:14320/1 +ATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTT ++ +CGFBDEH4AEF3AAFC7=EE;AEFFB;@;;;;;6@@ +@HISEQ1:121:C0EP5ACXX:8:1103:4920:91470/1 +AACCTTGGGTTGTGGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAG ++ +IJJJJJJJJFHBDDD9?@B>BD95?B@>BDDCDCDCDDDA38 +@HISEQ1:121:C0EP5ACXX:8:2106:16293:193745/1 +CCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGA ++ +AF:CF@@?EA??08?<05700>A>@>@8>888(+3)759BA<9>ABBBB05>B?7@@;;A:(+4:ABB@ +@HISEQ1:121:C0EP5ACXX:8:2102:17267:17939/1 +TCTAACCTTGGGTTGTGGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCNN ++ +IGDHGGIII@HG?CF?BFDHGGIJJDIJJEEGBHIGBB8@@CDDCCDADCDCCCDB>B>@DACDDB@D>B@@B@@ACCDCCDDDC@CDD5<5>A9ADD7 +@HISEQ1:121:C0EP5ACXX:8:1304:7828:90428/1 +GATCAAATAAATCAAACCGATCTAACCTTGGGTTGTGGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGC ++ +IJJJJIJJIJJJJJJIJJJJJJJJJJJIJIJJGHHFHIHIJIJJJHHHHFFFDDDDBBBBBCCDEDDDDDCDDDDDDDBDCDCDDD8 +@HISEQ1:121:C0EP5ACXX:8:1108:13629:82569/1 +TCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGG ++ +IIJJJGIDGHIIJI@BFFEFIDHH@FHGCF>FHGHIE@BGCE=GIJJIGIIG@AAED@@EF?CCEB>(45;>@CC1-2>A@CD?5:> +@HISEQ1:121:C0EP5ACXX:8:2303:21067:161452/1 +CTAACTCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTAAAGAGACTGTATTCTTCAGCAACAATCAGATCCCCAGATTGAT ++ +DHFH9CFEGGG)@GEGGIICH;BC@HBB9CCCCC3ACCCA>3>5;>:;5:@C99?(9:(+:(4(29CC>C +@HISEQ1:121:C0EP5ACXX:8:2102:4018:54516/1 +TAAACAAACTATAGAATTGAAACAAGAGCCACACCAGGAAAGAGCCTTGATCAAATAAATCAAACCGATCTAACCTTGGGTTGTGGT ++ +GHJJJJJJJJIJJJJJJJIJJJIJJDHHCGHIJJIIJIHIIIJJIDIIJJJJJGJGIIEFHEHFFFDADDDDAABDDDDD??DBBDD +@HISEQ1:121:C0EP5ACXX:8:1301:9106:149287/1 +ATAGTAAACAAACTATAGAATTGAAACAAGAGCCACACCAGGAAAGAGCCTTGATCAAATAAATCAAACCGATCTAACCTTGGGTTG ++ +GBHG?CCEEDCBHIICHGGGIJI@DGHGG@DH9BBDHBDFEIFHGIGII;=DEECHHECEB@DFFEECACBDB@B>:@BDCCCDBB@ +@HISEQ1:121:C0EP5ACXX:8:2107:3966:107043/1 +ACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGGCCTCCTCTGCTCCCTG ++ +JJJJJJJFHHJIIHHIIGGGIJIIFECHGIJJGG@GHCHIEFHIJJJJGJEHHCEH>AHHE?DFFFEDCCEDDDD?CDDDDCA@@?: +@HISEQ1:121:C0EP5ACXX:8:2207:2091:165857/1 +AATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGNNN ++ +IJJJJBHHJJIJIIGHJJEIJDHIDCHGJJIIJJJJJJJJJJIIJJJHHHFHGFFFFFFCCEEEEEDCAACCDDDDDDDCDDD@BDD +@HISEQ1:121:C0EP5ACXX:8:1201:14768:136485/1 +ATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTATAGAATTGAAACAAGAGCCACACCAGGAAAGAGCCTTGATCAAATANNN ++ +@HIIIIJJJIHHGC+A?EDG@ACCCAD@CCDDDDD@CCCD +@HISEQ1:121:C0EP5ACXX:8:2203:13818:80144/1 +CTAACTCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTAAAGAGACTGTATTCTTCAGCAACAATCAGATCCCCAGATTGATTT ++ +JIGEHJIJEGEGIJD;@@DH4BFGIJGJI>?DHGIIIFFFFE@CCEC5=CD;>CCCD@:@35>C<98>(:@C@>CDBC8ACC>CDC@ +@HISEQ1:121:C0EP5ACXX:8:2303:15336:10647/1 +ATCAGATCCAATTGATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTATAGAATTGAAACAAGAGCCACACCAGGAAAGAGCC ++ +GGGHFGGICHI@DHBFGIBGD>8DDBGEHJIGHIJIG>GHI@E@HGCCEH@CBCDFCEECCCE;?=?AB?ACCD?BD@8DHCCEIIJGEEFIGIIJGIIGGGGBGIGIGCDFEGHII@HHIDCGGGIGEGHI>CA?3=AE>D3@C>B>>C@@>;;@C +@HISEQ1:121:C0EP5ACXX:8:1204:20561:59058/1 +GACCTAAAGAGACTGTATTCTTCAGCAACAATCAGATCCCCAGATTGATTTGCTCTGATGGCCGCTCTTGAAGGAGTTTCGTTCCTC ++ +GIJJJIGIIEHGGCGGGGIEAHA>CEEDDDEDDC??@BDDDCCDCDDDADDDDDDCDDD +@HISEQ1:121:C0EP5ACXX:8:2302:16643:74025/1 +TCTCAGATCGGTGCTTGGTTCCCTCCTGGCCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATGGATTGAAGGCTGCTCTCACCGGN ++ +JJJJJJIJJJJFIJIIJJGGHJJIJJIJJJJIJJJJJJJJJJJJJJJJJHHHEDFFFFFCECEEDDDDDDDDCDDDDCCDDCDDDDD +@HISEQ1:121:C0EP5ACXX:8:1201:6783:137262/1 +TATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTNNNNNNNNNN ++ +JJJIJJIIJGJJJJJIJIJJJJIIJJHIIIEHJJIIJJJJHJIJJEGIJJHGFHGHHHFFFFFDDDBDDDBDDBBD9ACDDDDDCAA +@HISEQ1:121:C0EP5ACXX:8:1305:18884:19620/1 +AACACCATATTTCCGGATCCAATCAATCTCAAACCATGAGCGACAATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGCATAGG ++ +IJIGIIGIGHJIJJJJIGIGHIJIIJJIGGHHHHHFFFFFEDDDDDDDDD5>CDDDDDDDDCDEEDDDCDDDDDDEDDDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:2301:20719:86692/1 +GTAAGACTGAACGCAACACCATATTTCCGGATCCAATCAATCTCAAACCATGAGCGACAATAGGTGTTAAGGTTATCAGATCCNNNN ++ +;CFEGIII9FHGCHEHI9GHIEGGIGGIHBGGGE=EGC@HECEH>CFFFAC@?@CCC5::?@>:@:4>CCDEC>>CCCC< +@HISEQ1:121:C0EP5ACXX:8:2203:14371:65836/1 +ATCTGATAACCTTAACACCTATTGTCGCTCATGGTTTGAGATTGATTGGATCCGGAAATATGGTGTTGCGTTCAGTCTTACCGAGTN ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHJIJIIGIJIJJJJJJJJJJJIHHHFFEFDFDDDEDDDDDDFDDEEDDDDD88 +@HISEQ1:121:C0EP5ACXX:8:1301:10584:5300/1 +AAGGAATGAGATTACTTATAATATACTCGGTAAGACTGAACGCAACACCATATTTCCGGATCCAATCAATCTCAAACCATGAGCGAC ++ +IFHE9EGIIIG4EFHGEG?FEDGBGGCF@F;?BCHHGGEGGBFHIIIGHHEFE>BDF;>A>>ACCCDD@@ADDCDCCBDD:@CDDDD +@HISEQ1:121:C0EP5ACXX:8:2105:3982:74547/1 +CAACGAAAACAAGGAATGAGATTACTTATAATATACTCGGTAAGACTGAACGCAACACCATATTTCCGGATCCAATCAATCTCAAAC ++ +JJJJJGIJJJIFHGGHIGIJHIGGICHGJJJJJJJJJJJJCHHEIGGIIJII@AB>BFDCEEEEEFC?BBDBDCDCDDCDCCDDC>A +@HISEQ1:121:C0EP5ACXX:8:2106:6787:24507/1 +ATTGATTGGATCCGGAAATATGGTGTTGCGTTCAGTCTTACCGAGTATATTATAAGTAATCTCATTCCTTGTTTTCGTTGTAAGATT ++ +GGIIEJJIJJJIIJJIJJIIJJEDFHIIIJJJJIIFGIJJIGHEBCEHHGHGGHFFEEEFFEECEEEEEDDDDDDDBDACDD:C:AC +@HISEQ1:121:C0EP5ACXX:8:2201:3644:185103/1 +TCCTCTGCTCCCTGCGAATGGTGATTGGAGATGGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTN ++ +IGGGHIEHIJJGEGIJJJEHG0??DFHIFHGEHGICEHGIHHCGHGIIIGHGEED>BCEDDCCDAADDACC@CCC:;ADDA@CA?AA +@HISEQ1:121:C0EP5ACXX:8:2306:20358:147552/1 +TTCTAACTAGATTAGAATAAGCCAGGGAAACATAACTAATCTTACAACGAAAACAAGGAATGAGATTACTTATAATATACTCGGTNN ++ +JJIJIJJJJJGIIIJIJIJJIIHIIJJIIJGJJJJIJJJJIJIIIIJIJJJJHIJHHGHFFFFFCCECECEEDDEDED@ADDDDBB@ +@HISEQ1:121:C0EP5ACXX:8:2302:1563:56433/1 +ATCAATTCTAACTAGATTAGAATAAGCCAGGGAAACATAACTAATCTTACAACGAAAACAAGGAATGAGATTACTTATAATATACTC ++ +JJJJGIJJJJJJJJJJJJIJJJJJJJJJJJJJJJIIJJJJJJJJJJJJJJJJJJJJJHHHDBEFEEEEEEDDDDDDEDDDEEEEEEC +@HISEQ1:121:C0EP5ACXX:8:2305:17541:101277/1 +ATCAATTCTAACTAGATTAGAATAAGCCAGGGAAACATAACTAATCTTACAACGAAAACAAGGAATGAGATTACTTATAATATACTC ++ +JJJJIJJJJJJJJJJJJJJJIJJJJJJJIJJJIIJJJJJJJJJJJJJJJIIIIJIJJHHHFDFFEEEEEEDDDDCDEDDEFEFDEEC +@HISEQ1:121:C0EP5ACXX:8:2105:7286:178698/1 +GAAAGGATCAATTCTAACTAGATTAGAATAAGCCAGGGAAACATAACTAATCTTACAACGAAAACAAGGAATGAGATTACTTATNNN ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIIIJJJJJJJJJJJJJJJJJJHHHHFFFDEDEDDDDDDDDDDDDEDDE> +@HISEQ1:121:C0EP5ACXX:8:1305:8563:150819/1 +CAACATGCACAGTCTCAACTGGAAAGGATCAATTCTAACTAGATTAGAATAAGCCAGGGAAACATAACTAATCTTACAACGAAAACN ++ +IIGDBFGAFGGGBEAGEGEHGGHGGAFHHIGH:FHGAF@FCEGIIGEEHEEFFD:ACEECDCCC>?B?BBCB +@HISEQ1:121:C0EP5ACXX:8:2202:16059:23739/1 +TGAGATCCAACATGCACAGTCTCAACTGGAAAGGATCAATTCTAACTAGATTAGAATAAGCCAGGGAAACATAACTAATCTTACAAC ++ +JJJJJJJJJJJJJJIJJJJIJJIJJJJIJJJJJJJJJJJJJJJJJJIJJIJJJJJJJJIJJIIHHHHFFFFEEEEDCDDDDDEDDDD +@HISEQ1:121:C0EP5ACXX:8:1106:12563:12186/1 +AATTGATTCCAATAATACATCTAATCTTGAGATCCAACATGCACAGTCTCAACTGGAAAGGATCAATTCTAACTAGATTAGAATAAG ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHIJJJJJJJJJJJJJJJJJJJIJJJJJHHGHHFFFFFFFCECEEEDDDDDDD; +@HISEQ1:121:C0EP5ACXX:8:1101:19268:137461/1 +TTCTAATCTAGTTAGAATTGATCCTTTCCAGTTGAGACTGTGCATGTTGGATCTCAAGATTAGATGTATTATTGGAATCAATTTTGT ++ +IJJIIIJJJHGHIIIHIJJJGIJJJJJJJIIHIJHIBHJJIIJIHJHIJIFHGIGGCGFHCHGGIIHGIHEEHFFFDFF@DDECEEE +@HISEQ1:121:C0EP5ACXX:8:2303:2805:180545/1 +TTTGTTTACTATTTTCTATAACCCTATGCCTGCATCAATTGGATCTGATAACCTTAACACCTATTGTCGCTCATGGTTTGAGNNNNN ++ +IIIJIIJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJGJJJJJJJJJJHHHHFFFFEEEEDDDDDDDC +@HISEQ1:121:C0EP5ACXX:8:1106:12024:106184/1 +TGTTGGATCTCAAGATTAGATGTATTATTGGAATCAATTTTGTTGCTGCTCTGCAGGAGAGTGTGTTAGATAGATTCCTCTACCTTT ++ +JIJJJJJJJJJJJJGIJJJIJJFIGJJJJJJIJJJIJJJJJJJJJHIJIIJJIJIJIFHHIJHHHHGHHFFFFFFFEFDEEEEDDDC +@HISEQ1:121:C0EP5ACXX:8:1203:12551:9896/1 +GCTCTTTCCTGGTGTGGCTCTTGTTTCAATTCTATAGTTTGTTTACTATTTTCTATAACCCTATGCCTGCATCAATTGGATCTGATN ++ +IIEIIGIIJJJJ>CCC>?AC>CCCCC +@HISEQ1:121:C0EP5ACXX:8:2208:11196:39835/1 +CCTATTGTCGCTCATGGTTTGAGATTGATTGGATCCGGAAATATGGTGTTGCGTTCAGTCTTACCGAGTATATTAT ++ +AEB@E@IDH6B@81:?3?9;81:???D9BB9D?BGHIB7';@H@FACE=C?>E;>>@(;>9;;59A>CB:@ +@HISEQ1:121:C0EP5ACXX:8:1202:2784:55498/1 +AAGTCATAATTAAGACTATGCACTCTATGAATATCACTGAAGTTCTTCAACAGAATAATCACAAGGCTTGAGCAAAGGTAGAGGNNN ++ +JJJIIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJIJJJJJJJJIIJIJJJJJJIIJJIJJJHHHHFFFFF@@ACEEDDC +@HISEQ1:121:C0EP5ACXX:8:1308:6994:8081/1 +TCATAACCTAAGGAAAATACTTTATCAAAGTCATAATTAAGACTATGCACTCTATGAATATCACTGAAGTTCTTCAACAGNNNNNNN ++ +JJJJJJJJJJIJGJIJJGHIJJJJJJJJJJHHIJJJJJJJJJIJIIIGIJJJJJJIJGJJJHHIJJJJJHFHHHHHEFFFFFEEEE> diff -r 000000000000 -r 05c27700e5ca demo_files/daughter_2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/demo_files/daughter_2.fastq Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,516 @@ +@HISEQ1:121:C0EP5ACXX:8:1301:12962:135792/2 +ACGGGGCGAATCCCCACAATTTGCAAGGGCAAATTATGTGTTCCACCACAAAATGAAACAAGAAAGGAAAGAAAACAAGCACAGAGN ++ +IIJIIJJJJJIJJJJIJIJJIIJJJHHGHFFFFCEEEEEFFDDDEDDDDDDDDDDDDDDDDDDDDDBBDDDDDDDDDDDDDDDCCC? +@HISEQ1:121:C0EP5ACXX:8:1105:5390:32380/2 +ATACGGGGCGAATCCCCACAATTTGCAAGGGCAAATTATGTGTTCCACCACAAAATGAAACAAGAAAGGAAAGAAAACAAGCACANN ++ +GIIJJJJJIJJIJJJJJIIIJJJJIHHHHHFFFFDEEEEEEFFDDDEDDDDDABDDDDDDDDDDDDDDDDCCDDDD?C?BDDDDCDC +@HISEQ1:121:C0EP5ACXX:8:1301:11290:183940/2 +CGAATCCCCACAATTTGCAAGGGCAAATTATGTGTTCCACCACAAAATGAAACAAGAAAGGAAAGAAAACAAGCACANNNNNNNNNN ++ +IIJJJJJIIGFHHIJJJJIJJJJGIHHHHHFFBDEFCCDEEDDDDDDDDDDDDDBDDDDDDDDDDDDDDDDDDDDDDDCDDDDDBD8 +@HISEQ1:121:C0EP5ACXX:8:2207:5683:120579/2 +GGGCGAATCCCCACAATTTGCAAGGGCAAATTATGTGTTCCACCACAAAATGAAACAAGAAAGGAAAGAAAACAAGCACANNNNNNN ++ +JIIJI>GIIJJIGHIGIJJJIIJIHHHGFEFFFEEECEEEDEDDDDDDDDDDDDDDDDDDDCDDDDDDDDDCDDDDDBCDDDDBBD9 +@HISEQ1:121:C0EP5ACXX:8:1301:12479:185948/2 +AACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTNNNN ++ +JIJJJJJJIJJJGIIJHIIGIGIIJJIJJJJJJJJJJIJIJIJIGHIIHGHIGG@EEIIHEE?EHFFFFD:CCCCC?CBCBDDCDDD +@HISEQ1:121:C0EP5ACXX:8:2103:4989:50580/2 +GAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCCCCACAATTTGCAAGGGCAAA ++ +BEHIGIIGIIJIJFGIEHDGGGHI?FHIG?DBGHGHFGI8BGHGGGIJJIJ@CEEFHHFFDDBB>BDD?ADDDDCDDDECCDDBB78 +@HISEQ1:121:C0EP5ACXX:8:1202:1654:144608/2 +TTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTT ++ +GHHFIGIEIGIJHGIIJJGHHGIIIIHJGHFFHHIJGGFEHIGIIGIGGHIIJIJJDIJJDIFEHHFFF@>@A@CCACDBDDDDDC5 +@HISEQ1:121:C0EP5ACXX:8:2304:11218:150303/2 +TCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTC ++ +JIJJJJIJJJJIJIHHJJJJHIHIGHIIIIJJJIIJEHIJIIJJIJJIJIJJIJJJGHFHHHFFFFEDECEECBCCDDDDDDDDDD: +@HISEQ1:121:C0EP5ACXX:8:2102:13316:62111/2 +GGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCCC ++ +JJFGIHIIEGIJJJGHIJHGGEHIECGEHHIIJJJJCHIIJJI=CEEG@E@EFHFHHE;BDECDECEEDB?ACDEDDDD@BDDD?CD +@HISEQ1:121:C0EP5ACXX:8:1106:3218:101980/2 +AGCACCGATCTGAGAACCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTN ++ +JJJGIJJJIHEIIJGIIJJIJJHIGIJIIJJJIJJHHHHCFFDDEEEDEFDCCDDD>CCDDD2ACCDDHEHHEHEB99DG9BB;?F@FGIGCAA<@CDDCACCDA@C: +@HISEQ1:121:C0EP5ACXX:8:1104:20525:199060/2 +AGAGCAGCCTTCAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGN ++ +HIJJJJJIJJJJIJJJJIJJJJJGIJJJJHIGIIJJIIJJJJJJJJHHHFFFFDDDDDDDBDBDDDDDDDDDDBDDDDDDDCDDDDD +@HISEQ1:121:C0EP5ACXX:8:2207:17083:161210/2 +CGGTGAGAGCAGCCTTCAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGANNNN ++ +JJJFHHGIIJIIJJJJIIIJIIJJJIJJJJJJIGIIIEIIIJJIGGGFHGHFEBFDDDDDDBB?BBDDDDBBDDDDDDDDDCDDDCD +@HISEQ1:121:C0EP5ACXX:8:2104:7464:97678/2 +GCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTT ++ +D:EH@EDHAHHB;@B=A:;?;;AACA;@ +@HISEQ1:121:C0EP5ACXX:8:1106:9192:29781/2 +TTCCGGTGAGAGCAGCCTTCAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCNNNNNNNN ++ +JJJJJICGIJJJJIJIJJIJJJIJJJJIJJJIGJJJHIIJJJJJJIJJJHHFFFFFEDDDDDDDDDDDBDDDDDD?BDDB>>BBCDC +@HISEQ1:121:C0EP5ACXX:8:2302:12102:76322/2 +TTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTT ++ +IJJJJJJJJIJIIJJJJIIJGGIIJIIJGIIIJJJJIIGHIJJJJJJJIJIJJJJJIIJJJJHH3?EDECCC@ACEDDCACDDDDDA +@HISEQ1:121:C0EP5ACXX:8:1202:10923:67043/2 +AGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTTCAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAA ++ +IEEHIGHIJ?DEIGIJIIJJGIGFFFHIIIJIGGEFHGHGHIJHHHHHHFDDDDDBDDDDDDDBDDDABBDDDDBA +@HISEQ1:121:C0EP5ACXX:8:2303:8797:124341/2 +AGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTTCAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAA ++ +HIJJIIIJJHIEIGIIIIJJGIJ?GHIHIJJIIJJJHGGIJJJJIJIIJIJJJJHHHHHHFFCCDDDDDDDD?ABAB@BBBDDDB@>@DFFCA>>:@;;BCA?15<)2?B?8< +@HISEQ1:121:C0EP5ACXX:8:2205:17966:149411/2 +CTCTAAAACGCTCTCTCCTCTCTCTACAGTGTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCT ++ +JJIJJJJJJJJJJJJJJJJJIJJJJIIJJIIIJJIJHHIJJJJJJJJJJJIIJJJJHJIIGGCEHFFFFFFECDDEDCDDCDDDDCA +@HISEQ1:121:C0EP5ACXX:8:2204:7913:47072/2 +TCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTTCAATCAATCTCCAATCACC ++ +JIIJJIHGHIHEHDHHGGEHBBGGIGHGGHIJJGGIGIH;F=FBFHHECGHIIIJ:BEEECBEEEDEDDDCDDDDDCDDDCACAACC +@HISEQ1:121:C0EP5ACXX:8:1206:14809:89750/2 +AAAACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGC ++ +GGGIEHHIIIGIGHGGHIDGIIHDHC@@C?3?ABCCC: +@HISEQ1:121:C0EP5ACXX:8:1107:8614:188228/2 +TTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCA ++ +HJIIGIJJIJIEIIGIFHII>GGIIJHGHHDIJJGGGHHEGIJJJIGGHGIIJIHFHEHFEEDDD@A:CCDDDBBBDCCCDDCCA?A +@HISEQ1:121:C0EP5ACXX:8:1207:13629:148866/2 +TCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGATCTCAGATCGGTGCTTGGTTCCCTCCTGN ++ +;EGH@=;AA>AC9 +@HISEQ1:121:C0EP5ACXX:8:1302:20544:36891/2 +TGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTTCAATCCA ++ +GIIJIJJJJJJJJJJJJJJJJJIJJIJJJIJHIJIJGHJIJHHHHHGFFFFEDCEEEDDDDDCDFDD=BDDDDDCCDDDDDDDEDDC +@HISEQ1:121:C0EP5ACXX:8:1201:13712:106244/2 +AGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTT ++ +IIJJJJCGIIJGIIIJJIJJIJJJJIIIJJJJJJIJJIHHHHHHFFFFFFEEEEEDDDDDCDDEDDDDCDDEDD@@BDDDDDDDDC: +@HISEQ1:121:C0EP5ACXX:8:1205:1987:169105/2 +GAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGA ++ +HHGBHGHJJIDDDGGIIEAFGDCAEEHIHGICHIGHEHFDF@B;BCCECECDDDCDDDDCDDDBB>ACD@CDDCCDECD55?<@ +@HISEQ1:121:C0EP5ACXX:8:1304:10703:43081/2 +TCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGANN ++ +?HIJGIHHHIJJJI?AHGIAGIGIJFGCEEHHHHFFDDCEEEDDDD3>CDDDDDDCCDDDDDDDDDDD@CCDDDD9(4>CCB9BFA(7<88..=C@67667)).7;@?;83>>;6;CC@@C>;5@,:(:>:>@:52(82(:3444:2<4:4>A@ +@HISEQ1:121:C0EP5ACXX:8:2202:11034:3947/2 +GCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTC ++ +JJJJJJJGHIIJGIEHGIIJJJ;BEAEBEEFFFEDDCDDEEDDDDDDDDDDDDDCC>ACDCDCDDDDDDDCDBBDDCCCDCA<3:AC +@HISEQ1:121:C0EP5ACXX:8:1101:3334:33169/2 +TCCTCTAAAACGCTCTCTCCTCTCTCTACAGTGGCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCT ++ +GIIIJBEDH@:3C+11:?F9C?FF@?<*?:**0*)(*/*9E<======))84@4@=7@7=)(((.;@;BCC((.;@@@ +@HISEQ1:121:C0EP5ACXX:8:2104:7518:85500/2 +AGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAG ++ +HIGI>FHGGEGGBHIBH1BFDC49=)./8B44-9>9.6;@@CB9??CCDDDCD>?:5+>>4@:?@(:ACCA@(9AC4:>CC@BDD? +@HISEQ1:121:C0EP5ACXX:8:2104:18741:150825/2 +CTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGC ++ +JJJJJJJFIIIJJIJJJJJIJGHHJIGIGIGHJJJHEACEDCDDDDDCDDDDDEEDDEDDDDDDDDDDCCDDDDDDCCCCDDDDDD@ +@HISEQ1:121:C0EP5ACXX:8:2103:17562:161306/2 +CTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATT ++ +HIJGGHCCHGGCEGEDBCGGEDCGDFEFDC@AA?>8;?CCDDD@>CC:4:?CCCC>C> +@HISEQ1:121:C0EP5ACXX:8:2303:4331:138576/2 +TTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAN ++ +IJIJJJJIIJICF@HIBGHIGDHHGIBFHIIIJJGIGGHIEHFFF?D@CCCC>@D;?B>C>@>CCDA +@HISEQ1:121:C0EP5ACXX:8:1206:16241:142787/2 +TTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGNNNN ++ +I@FHECFGIJJGHGGHHCHDHFHEEHIIJIIJGIEIJIIJJJJIJJIJJJIIGJIIJGEEHHFE=;?@DED>CEDDDDBD@CDBCDC +@HISEQ1:121:C0EP5ACXX:8:2305:14287:109430/2 +GTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCA ++ +IJJJJJJJJIJJJIJIJGIJJIJJJJJHIJJJJJJJIJJJJHHHFFFFEFEEDEDD8;BCCCDDDDDCBDDCDEEDDEDDDDDDDD: +@HISEQ1:121:C0EP5ACXX:8:2107:12104:180859/2 +CTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTT ++ +4ADBBD@CHHIB?99?B1/88C;;>>>CCA>3;3ACCDA:@ +@HISEQ1:121:C0EP5ACXX:8:2306:14745:2012/2 +GGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTC ++ +JJIJJJIJHIIIHGIGGHGGIGJJIIGGIGIJJEIGHHGGEGHIIIHHHDD?=?BCD@C>CCCCBDD09@CDCDDCCD??8?C@CC> +@HISEQ1:121:C0EP5ACXX:8:1107:19971:96047/2 +ATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTC ++ +JJJJJJJJIJJJJHJIJJJJJJIIIJJJJIJJJJJJIJJJJJJGHJJJJGHFFFFDDCBDDCCCCDDDDDDD<8>'2;3,,;AC?ACCFFCCEAECC<5=CBDDDA@A +@HISEQ1:121:C0EP5ACXX:8:2106:9872:27596/2 +AATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGN ++ +JIJJJJGIJJJJJJJJJJGIJJEIGIJJIIJJJJIJIJIIJJJJJJIJIIIJJHFFDDDCBDBBDDDDDCDDDDDDB5F?6D&6:28@A +@HISEQ1:121:C0EP5ACXX:8:1206:4841:180732/2 +GAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGANN ++ +IIJIJJJJJJJJJJJIJJJJJJJIIJJJJJJIJJJJGIJJJJJJJHHHHHFFFFFEFDEEEEEDDCCBDDDBDDDDDDDBDDCDDDC +@HISEQ1:121:C0EP5ACXX:8:2104:5669:156581/2 +GAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGANN ++ +JIJJJJJJJJJIJJJJGIJJJJJJJJJIJIJJJJJIGIJJJJJIJFFHHHFFFFFFFEECEEEDDCDDDDDDDDDDDDDDDDCC>A@ +@HISEQ1:121:C0EP5ACXX:8:1203:5383:144796/2 +GAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTG ++ +HBB;CFEG?FGGG@GIBBGGHHBG@FIGDH6>>@>B@@B595ACBB<<>CC +@HISEQ1:121:C0EP5ACXX:8:1201:18290:177436/2 +TCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCANN ++ +IIIGJJIIIIIIGEBCFHIGIJGHIIIJJHHHIFHEDGGIJJJGJIJHIIJBHGAHFE;;B@BEDEDEDDDDDCBDDDB?CDCAAC@ +@HISEQ1:121:C0EP5ACXX:8:1207:3038:16038/2 +TTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGNNNN ++ +IIIEEHFHCFDCD>EEEA?DD@DA>A3;3;3,;?CCD1>?> +@HISEQ1:121:C0EP5ACXX:8:1206:16810:160141/2 +ACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGT ++ +JJIIGGIIHGGIIIJJGIGGIJJJJJIGIIGIGIEGFHIJIIJJJIGGGEIC;DGIJIGHHGHFFDB@CCEEDA@@AA@5<@DCDBC +@HISEQ1:121:C0EP5ACXX:8:2108:13659:50707/2 +TTACCCATCAACAATTAACACTTACTTTAAAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGNNNN ++ +GEFI3A+3B@CDDECDDCCDCDDDDDC>CDD>ACC +@HISEQ1:121:C0EP5ACXX:8:1101:8737:95819/2 +AGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTT ++ +JJJJIIIGIJIJJJIJJJJIJIIGIJJIHHHFDDBDCDDCDDDDCCDDDDDDEDDDBDDDDCEDDDDDDDCCCDDDDDDDDCCDDDC +@HISEQ1:121:C0EP5ACXX:8:1301:15961:111397/2 +TCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTAT ++ +IIGIHGIIFGIIIGHIJJIIIIJIIJFGHJHGIJGIHIHJHIJJIJJJJJJJJJJJJJJGHHHHEFFFFFFCBD=@CCDDDDD>>>B +@HISEQ1:121:C0EP5ACXX:8:1302:19521:69299/2 +GCCTAGGATGGAGCTTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACAAATAATTTGCCC ++ +C:AACACD +@HISEQ1:121:C0EP5ACXX:8:1203:3175:113512/2 +TACCCAAAACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTAGCTCCCAGGTTCTCANNNNNN ++ +GIIIIJJCGIHGJJGGIGGEHIJJE@FEHGIJEEAF@FHIIJIGEHEEAEHEEHFEEFFFDE>A@(,>ACDDDD?@ACCDDDDAC?< +@HISEQ1:121:C0EP5ACXX:8:1208:3501:162441/2 +GGAACTAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCCATCTGGGGATCGGATTGTTGGTGAAGAATACAGTC ++ +HG<@G**?F;CBBHGACGBDGGIIII@FH;B;C9A>ECE)7@;>DECBB>?';?DD<@:9(+8@@@39:C@C>>C +@HISEQ1:121:C0EP5ACXX:8:2102:10284:25123/2 +AAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAAT ++ +AFABB:;@BE;CGH>==CHHDD'9;;=CC:>@C>CCCCCDCCCC@C<>85(4>CDA:@3?AAA@C:>?@ +@HISEQ1:121:C0EP5ACXX:8:1102:16158:78675/2 +CTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAA ++ +JJJJJJJJJJIJJJJJJJJJJIJIJGJIJHHHHHHFFFFFEDDDDDDDDDDDDDDDDDDDDDDEDDDDDDDDDEDDDDDCCCDCCCC +@HISEQ1:121:C0EP5ACXX:8:1203:3978:188625/2 +CTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAA ++ +GGIGIIFII@EHD>CDHE0@A@FAGEGBDDCC:A>@CC3>:AC>CCA@CCD<5?CCCD@C>CAAA>ACACC +@HISEQ1:121:C0EP5ACXX:8:2302:10875:119470/2 +CTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAA ++ +JJJJIIJIIJIJJIIJIJIJJEGGJGIIEEHHHHHFEFFFDDDDDDDDDCDDDDDDDDDDDDDCCCDD>BDDCDCD>AACCDCDDCC +@HISEQ1:121:C0EP5ACXX:8:1302:7021:199313/2 +AGATGGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAAC ++ +IJIJJJJJJIIIJJJJIJJJIJJJJJJIJJJIJJJJHIIJJIJGJGIJJIIJJEHCHHHHHFFFFFEEEEED>CCB@ACCCDDDACB +@HISEQ1:121:C0EP5ACXX:8:1306:10437:150125/2 +TCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCANNNN ++ +JJJJJJJIJJIJJJJJJJJJIIIJJJJJJJJJIIJHDGIJJJJIJJJJJIJJIHHHGHFFFFFCEEEEDDDDDDDDDDCDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:1202:7387:154438/2 +CGGTGCTTGGTTCCCTCCTGGCCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATGGATTGAAGGCTGCTCTCACCGGAATCTCTTC ++ +JJJGIJJIJIHIJJJJJJIIJJJJJJIJIIHIJJHIIIIGGIJJCGEEHHHEFFFFFEDEECEDDDDDDDDCCDDDBB@9?CDDEC> +@HISEQ1:121:C0EP5ACXX:8:2103:12603:82497/2 +AAGCCCTAACTCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTAAAGAGACTGTATTCTTCAGCAACAATCAGATCCCCANNNN ++ +JIIIJJJJJJJIIJGJJJJJIJJJJIJIGGIIHIJIIIIJJHFDDDCDDDDDDDDDCEEEEFEDEDDDDD?BCDDDDDDDDD?@BCC +@HISEQ1:121:C0EP5ACXX:8:2104:11050:81554/2 +AACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTN ++ +@CDDDDDDACB6BD6?BDDCDDDB9B6BA@BBD@DCCD3>AACCBCBDDDBCCDDDC?C?C@CCDDDDEDDDBBDAAACC@@CBDD@ +@HISEQ1:121:C0EP5ACXX:8:2106:4110:37086/2 +GGATGGAGCTTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCA ++ +IIIIIJEHIIIJJJIIJJIIJJIHIIEDGHIIIJIJGHJJJIIIJJJIIGHIIIIIIIJBHHHBDEDEDEEDDDCDEECDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:1103:1762:125454/2 +GGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGNNNNNN ++ +JD@BDDDDDEDDDDDDCCDCDDDDDDDDCDDBDDDDBBDDDDDCDCAACEDCB?@BCC +@HISEQ1:121:C0EP5ACXX:8:1101:15305:126129/2 +GAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGN ++ +JJJJJJJID9@B@CDDEDDDDCDDDDDDDDDDDDDDCDDDDDDBDDDDDDDDDDCDDDDDDDCDBBD@DDCDDDDA8?59359CAAC@CA@?C>@:AACCC +@HISEQ1:121:C0EP5ACXX:8:1102:18712:9225/2 +GCTCCCTGCGAATGGTGATTGGAGATGGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAN ++ +JJJGJJJIIJJJJIJDHIGIJJFHHGGJGIIIIJEGHHGDHGIAEGIBHFFFBDFEEEEEDECCCACCCCCDDDC@CACCCDDCCCC +@HISEQ1:121:C0EP5ACXX:8:1102:11058:174357/2 +GGATGGAGCTTTTGCTCCTCCCCTCTGTGCTCGTTTTCTTTCCTTTCTTGTTTCATTTGTGGTGGAACACATAATTTGCCCTTGCAA ++ +JJIJJJGIJIJJJJJJIJIIFHIJJJJIDIJJIEGIHIJJJIJGJJJJJIHIJIHHGHHHHF@BDBCACEDDCDDDECCDDDCDCDD +@HISEQ1:121:C0EP5ACXX:8:2206:15398:115295/2 +CCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAAT ++ +JJJJIIIIGIGFIJJJD3@D@>A@CCD@CCDCDDDDDDDDDDDDDAA@B<@>C@C@CD@33:<9@BB>>CCAA>A?:?C +@HISEQ1:121:C0EP5ACXX:8:1108:5820:79317/2 +CACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCCAATTGAAGCCCTAACTCAACCCCCTATCTCAGATCCGATGCTCGGCNNNN ++ +JJJJIJJJJJIJJJJJJJJJHJJJJJJJJJJIJIJJIIJIJIJJJJJJJIJJJJJJHHHFFFDEEEEDDCDDDBBDDDDDDDDDBDB +@HISEQ1:121:C0EP5ACXX:8:1106:6069:149613/2 +GGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCANNNN ++ +IJHIJIGIIIJIJIIIGIJJD-:9BDDDEDDDDDDDCDDDDDDDDDCDDDDBDDDDDDDBDB5CCDDCCDDCCDDD@BBBCDCACD? +@HISEQ1:121:C0EP5ACXX:8:1106:6337:118237/2 +TGTGGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAN ++ +IJIIJIJJJJJGHHIJCHHIJJJD5BDBDDDEDDDDDDDDDDDDDDDDDC?ABBD5;BBDDDDDDD:ADDDDCCCCB9>>@BBDCD: +@HISEQ1:121:C0EP5ACXX:8:1303:16108:108202/2 +GTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAATAGCGGCCATCAG ++ +79:69C>>BC>((+8388@77BBBDC(::45-&05>?CC +@HISEQ1:121:C0EP5ACXX:8:1106:16181:135878/2 +GGTTGTGGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCACGAGCGGCCAT ++ +2CACE8C?GG>@?F>))1??6B0)(7-7<00>CCCCCCCCCCCDC&5<7BC8+9328;&5-9AAB@DBDDCCC:>:(8(5>@9>BDC +@HISEQ1:121:C0EP5ACXX:8:1107:11975:14320/2 +CAGCAACGAAGGGGGGATGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCC ++ +FHIIEC;F)):?@@F1&0883>8>((833>AC>(5)595>8(9>?8:@C4>:CCCDDDDDDCBDDDDCCDDDD +@HISEQ1:121:C0EP5ACXX:8:2106:16293:193745/2 +ACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCG ++ +BD3CC4C<3C>@CDCDDC? +@HISEQ1:121:C0EP5ACXX:8:2102:17267:17939/2 +CTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTAAAGAGACTGTATTCTTCAN ++ +EGIIJIBHGHIGIIJBFCHG9DB49CEGEGCDGIGBDHIIIG=@>FECHHEEHCC>DFFCDC88;5>:>CDCC3CCDEEC3:> +@HISEQ1:121:C0EP5ACXX:8:1101:9236:28777/2 +GGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTAAAGAGACTGTATTC ++ +IJIJJJJJJJJJIIJJJJJJJIJJJJJJIHIJIIJDGHIICHJJJIEIIJJGHGHHGFFFDDEEDBDD@>BD3>@CDDDDDD@CDDA +@HISEQ1:121:C0EP5ACXX:8:1304:7828:90428/2 +TTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCA ++ +IJJJJIJGIJJIJIIEEEGGEBHCHFGHIJIGEHGHHDHIJJJJJEHIIDHIIIEBEFEEFFDD>BDDDCCCDBABDDCD@CACCC> +@HISEQ1:121:C0EP5ACXX:8:1108:13629:82569/2 +AATTGAAACAAGAGCCACACCAGGAAAGAGCCTTGATCAAATAAATCAAACCGATCTAACCTTGGGTTGTGGTTCCAGCAACGAAN ++ +GGG@BHHBHFFBFHH3CEGA@GD=BDE8?GCDFBFFA>=CFHHIICHGHCE@EH>>2;6(..;(-((,38??58@:@49??<<@7< +@HISEQ1:121:C0EP5ACXX:8:2303:21067:161452/2 +ACCAGGAAAGAGCCTTGATCAAATAAATCAAACCGATCTAACCTTGGGTTGTGGTTCAAGCAACGAAG ++ +J;CCGHFHCBEHG8;@F4@DC43A(;9?7?AC>;@CDDDD6@7? +@HISEQ1:121:C0EP5ACXX:8:2102:4018:54516/2 +ATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATTGGTGCTTGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTNNN ++ +IJIIJJJJJJJJJJJIIJJIJIIIGJJGIIDHIIJIGHIJJJHIJJJJJJIHIJJJJIGHHGFEFFFEDECEEDDDDDD?BDD>@@C +@HISEQ1:121:C0EP5ACXX:8:1301:9106:149287/2 +AGATCCCCAGATTGATTTGCTCTGATGGCCGCTCTTGAAGGAGTTTCGTTCCTCGCCTCTGTTTTCGCAAGGAGTTATGGACAACCC ++ +GIIIGIIGAE@FHIJGHJJJGGHHFIIGHGHIEIHIFAHHIGD7@EGGIEEHHFFFAABCC@;CDCBBDBDDAA39ADCD>@AAD?BB@BDC4@8 +@HISEQ1:121:C0EP5ACXX:8:2207:2091:165857/2 +TAGAAAATAGTAAACAAACTATAGAATTGAAACAAGAGCCACACCAGGAAAGAGCCTTGATCAAATAAATCAAACCGATCTAA ++ +HHHG?CFGHHFEGDCBDGCF@DC976?AECE@DD;;>@>>>AC@C?:8???AC +@HISEQ1:121:C0EP5ACXX:8:1201:14768:136485/2 +TGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCC ++ +@EHEHHEGHEGCFGCGBEG>GGCHJGB@FADH;@ADB@).7CEECE==ECBB@;?@@(636=;>C@>:9@@A9 +@HISEQ1:121:C0EP5ACXX:8:2203:13818:80144/2 +ATTGATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTATAGAATTGAAACAAGAGCCACACCAGGAAAGAGCCTTGATCAAAT ++ +IJJJHJJIIJJJJJJJIJDHIGGIHIJIJJG@GIJGFHCGIIHIJJIGGJHIHIIIIEHIJHHHHFFFD=AE@CCC=CD@CCCEDD> +@HISEQ1:121:C0EP5ACXX:8:2303:15336:10647/2 +ATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTAAAGAGACTGT ++ +FDHHIJGH3CAFHIIJEGEHAHEFG:CDF?:5=-5>BACCDCDCCCC: +@HISEQ1:121:C0EP5ACXX:8:2106:17975:106193/2 +CCAGATTGATTTGCTCTGATGGCCGCTCTTGAAGGAGTTTCGTTCCTCGCCTCTGTTTTCGCAAGGAGTTATGGACAACCCCCCTTC ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFHIJJJIIJJHHFFFFDCEEEEDDDDDDDDCDDEDDDDDDDDDDDDDB< +@HISEQ1:121:C0EP5ACXX:8:1305:8510:135015/2 +CAAGGAGTTATGGACAACCCCCCTTCGTTGCTGGAACCACAACCCAAGGTTAGATCGGTTTGATTTATTTGATCAAGGCTCTTTCCT ++ +JJGIIGIEHIGIJGIIHHIJJJJGIIIGIIIJGIGIHHFHFFFFDDDDD@CDDDDDDD?@BDDDDEDDDEDDCCDCCDDCBCDDDDC +@HISEQ1:121:C0EP5ACXX:8:1208:6964:75542/2 +ATAGTTTGTTTACTATTTTCTATAACCCTATGCCTGCATCAATTGGATCTGATAACCTTAACACCTATTGTCGCTCATGGTTTGAN ++ +GB>F4I@I;FECG9HHIJJ>HEBFGGEFDDHDH@CEBGGI:BGHIGBBFCDGGGGGJJIGGGHHGIIHGGFEF=BE?CEC@C=?;? +@HISEQ1:121:C0EP5ACXX:8:1204:20561:59058/2 +TCTCAAACCATGAGCGACAATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTAT ++ +JIG:BHHIIJJA@>A?CCACCCAC@C>B@CCCABBC@> +@HISEQ1:121:C0EP5ACXX:8:2303:7038:46610/2 +TAGATCGGTTTGATTTATTTGATCAAGGCTCTTTCCTGGTGTGGCTCTTGTTTCAATTCTATAGTTTGTTTACTATTTTCTATAACC ++ +HJJIJJJJHIJIIJJJJJJJJIJJJJJJGJJJJJJJHIJFHFHIJIJIJIHFFEEHHHFFFFFFDFEEEEECDDEEEEEED@D@CCC +@HISEQ1:121:C0EP5ACXX:8:2304:2164:16073/2 +TCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTAAAGAGACTGTATTCTTCAGCAACAATCAGATCCCCAGATTGATTTGCTCT ++ +JHIJGGIIJJJJJJJJJGIIJJHIIJFJGGIJIIHHFFFFFFEEEEEEEEEFEDEDDCDDDDDCDDDDDDDDDDBDDDDADECDDDD +@HISEQ1:121:C0EP5ACXX:8:2302:16643:74025/2 +GTTTACTATTTTCTATAACCCTATGCCTGCGACAATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGCATAGGGTTATAGAAAA ++ +JJJJJJJJJJJJJIJJJJJJJJJJJJJIJJJIIJIJJJIBDFHGIJJHIJIJJJJJJJHHHHHHFFFFFFDDDEDDDABDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:1201:6783:137262/2 +ATATTTCCGGATCCAATCAATCTCAAACCATGAGCGACAATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGCATAGGGTTATA ++ +JJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJIJJIIHHHHH@DEFFFEEEEEEDEEDDDDDDDDCC@ACCDBDBDCDDDCBBC@ +@HISEQ1:121:C0EP5ACXX:8:1305:18884:19620/2 +CTCTGATGGCCGCTCTTGAAGGAGTTTCGTTCCTCGCCTCTGTTTTCGCAAGGAGTTATGGACAACCCCCCTTCGTTGCTGGAACCA ++ +JJJJJJJJIIJJIJJJJJJJJJJJFHIJGIIFHIJJJHIIJJJJJHHHHFFDDEDDDDEDDDDDDDDDBDDDDDDDDDBCDDBDDD8 +@HISEQ1:121:C0EP5ACXX:8:2301:20719:86692/2 +CGCAAGGAGTTATGGACAACCCCCCTTCGTTGCTGGAACCACAACCCAAGGTTAGATCGGTTTGATTTATTTGATCAAGGCTCTTTC ++ +HIAEEIICGEGIIG@?FHI3:?@DFFE>FEGGEC3?ACCBBDDDBCD?;AB3(>>C@C@BA?AAC> +@HISEQ1:121:C0EP5ACXX:8:2203:14371:65836/2 +GATGGTAATAAAGTCTAGAAATGAAATACTCATAACCTAAGGAAAATACTTTATCAAAGTCATAATTAAGACTATGCACTCTATGAA ++ +JJJJJGIIIJJJJIJJJJJJJJJJJJJJJJJJJJJJIJJJIJJJJJJIJJJJJJJJJJJHHIJHHHHHHHFFFFFFCEEEEEDDEDC +@HISEQ1:121:C0EP5ACXX:8:1301:10584:5300/2 +CGTTGCTGGAACCACAACCCAAGGTTAGATCGGTTTGATTTATTTGATCAAGGCTCTTTCCTGGTGTGGCTCTTGTTTCAATTCTA ++ +HI?FFFGC<1?;H>FHIJIFGEIFBGGIAHGEBCBA5?>BD?BBDEE>CED??@BA?>A>:++<:@:>@CDC +@HISEQ1:121:C0EP5ACXX:8:2105:3982:74547/2 +AGATCGGTTTGATTTATTTGATCAAGGCTCTTTCCTGGTGTGGCTCTTGTTTCAATTCTATAGTTTGTTTACTATTTTCTATAACCC ++ +EHHGHIFGHIIDFGIIJJJIGHGIGIGIJIJJJIJJIFBFFHGEGHGHGHHFH?AEEHFCDBEBFFCEEEEDDDDEECACCDCC@CB +@HISEQ1:121:C0EP5ACXX:8:2106:6787:24507/2 +CTTGAGTCCACAAGGAAGGCATGTAATGTTAATAAAATTCAAATTATGTAATTTCAGCTTACAAATCAAAGATCGAAGGANNNNNNN ++ +IJIJJIBHHIJJJIIJIJIJJJJFHIGGIJJJIEIIHJJJJIJHJJJJIIGIJJJJJIIIJJJEGHHHHHHHFFFFEDCCBBCCA;@ +@HISEQ1:121:C0EP5ACXX:8:2201:3644:185103/2 +TACTTATAATATACTCGGTAAGACTGAACGCAA ++ +*?CDD<4B9?9B@@99D=/?;88)==8==@EBA +@HISEQ1:121:C0EP5ACXX:8:2306:20358:147552/2 +ATTGAAGCCCTAACTCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTAAAGAGACTGTATTCTTCAGCAACAATCAGATCCCCA ++ +IJJJJJIJIJIJIIJJJIFIJJJIGIJJJDHIIHHIGHIJJIIJHEDDDDCCCDDDDDDDCDDDDEDCDACCDDDDDC>CCACCDD< +@HISEQ1:121:C0EP5ACXX:8:2302:1563:56433/2 +GGCTCTTGTTTCAATTCTATAGTTTGTTTACTATTTTCTATAACCCTATGCCTGCATCAATTGGATCTGATAACCTTAACACCTATT ++ +HIJIJJIJJJJICHIJJJJJFIGIEGGHIIIJIJJJIIJJJIJIJJJIJJJJJJJIIIIIJJJJHHHHHHFFFFFFEEEEEEDDDDC +@HISEQ1:121:C0EP5ACXX:8:2305:17541:101277/2 +CAAGGAGTTATGGACAACCCCCCTTCGTTGCTGGAACCACAACCCAAGGTTAGATCGGTTTGATTTATTTGATCAAGGCTCTTTCCT ++ +JJJJJIJEHGIIJJJJJJJJJGIJJJIHGIJJIJIIHHHHFFFFDDDDB@CDDDDDDD?BDDDDDEDEDEDDDDEDCDBDDDDDDDC +@HISEQ1:121:C0EP5ACXX:8:2105:7286:178698/2 +TTTGTTTACTATTTTCTATAACCCTATGCCTGCATCAATTGGATCTGATAACCTTAACACCTATTGTCGCTCATGGGTTGAGATTNN ++ +IJJIJJJJJJJJJJJJJJJIJJJJJJJJJJJJJIIJJJJJJJIJJJJJIJJJJJJJJJIJJJJIJJIHHHHFFFFEDCCDCDDDDD@ +@HISEQ1:121:C0EP5ACXX:8:1305:8563:150819/2 +CCTTAACACCTATTGTCGCTCATGGTTTGAGATTGATTGGATCCGGAAATATGGTGTTGCGTTCAGTCTTACCGAGTATATTATAAN ++ +EGIIGAHIIIIHIGIIIIJJJJJJIDHHGGIAEHIHIIICHIIIGD@GBGGHEFEEEDBEDADBCDFDDEECCB=?@ACDDDDDAC@ +@HISEQ1:121:C0EP5ACXX:8:2202:16059:23739/2 +TCAGCAACAATCAGATCCCCAGATTGATTTGCTCTGATGGCCGCTCTTGAAGGAGTTTCGTTCCTCGCCTCTGTTTTCGCAAGGAGT ++ +JJJJJJJIIJJJJJJJJIJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJIJJIFHCHFFFFFDCCCDDD@DDCCDDDC?B@DDDBDD +@HISEQ1:121:C0EP5ACXX:8:1106:12563:12186/2 +CTCGCCTCTGTTTTCGCAAGGAGTTATGGACAACCCCCCTTCGTTGCTGGAACCACAACCCAAGGTTAGATCGGTTTGATTTATTTN ++ +JJJJJJIIJIJJJJJJJJJJJIJIIJJJJJJJJJJJJHFFFFDEEEDDDDDDDDDDDDDDDDDDDCCDDDDDDDBDDDDDDEDEDEA +@HISEQ1:121:C0EP5ACXX:8:1101:19268:137461/2 +ATGAAATACTCATAACCTAAGGAAAATACTTTATCAAAGTCATAATTAAGACTATGCACTCTATGAATATCACTGAAGTTCTTCAAC ++ +GHBHHHIIJJJJJJJJJJJJJJIJJIIJJJJJJJJIIJJHIJJGGJJJJJJJJJJJJIJJJJGIJIIJJIEFHHHFHFCFFFFFEEC +@HISEQ1:121:C0EP5ACXX:8:2303:2805:180545/2 +CAACAAAATTGATTCCAATAATACATCTAATCTTGAGATCCAACATGCACAGTCTCAACTGGAAAGGATCAATTCTAACTAGATTAN ++ +JJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJHHHHHFFFFFEEEEEEEDDDDDDEDC +@HISEQ1:121:C0EP5ACXX:8:1106:12024:106184/2 +ATAAAATTCAAATTATGTAATTTCAGCTTACAAATCAAAGATCGAAGGAGATGGTAATAAAGTCTAGAAATGAAATACTCATAACCT ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJGHJJJJJJHIJJJHFHHHHFFFFFFEEEEEEE@ +@HISEQ1:121:C0EP5ACXX:8:1203:12551:9896/2 +TTCAACAGAATAATCACAAGGCTTGAGCAAAGGTAGAGGAATCTATCTAACACACTCTCCTGCAGAGCAGCAACAAAATTGATTCCA ++ +GIHGGIIIJFIGGGADHIIEGIGGIIIGGIJIJ9BFCFGEGEHEDHGIJIJJIIGIJJJHHHGHFFFFFEEECEDDDDDDDCDCDFD +@HISEQ1:121:C0EP5ACXX:8:2302:5053:188424/2 +TTTTGTTGCTGCTCTGCAGGAGAGTGTGTTAGATAGATTCCTCTACCTTTGCTCAAGCCTTGTGATTATTCTGTTGAAGAACTTCAN ++ +JJIJJJJJJJJIGGIJJIJJEHDHCFDGGIJJIIJIIIIJJJJJJJJJJJJJJJJIJJJIJJEHHHEHHFFFFFFFECDDCEDDDDC +@HISEQ1:121:C0EP5ACXX:8:1203:12097:70095/2 +CTGAAGTTCTTCAACAGAATAATCACAAGGCTTGAGCAAAGGTAGAGGAATCTATCTAACACACTCTCCTGCAGAGCAGCAACAAAA ++ +JJJJJJJHIJJJJJJJJJJJJJJJJJJJJJJJJJJJHHIIJJFGHIJJIJJJJJIJJEIIJJJHHHHDFFFFDEDDEDDDDDDDABB +@HISEQ1:121:C0EP5ACXX:8:1305:18243:121070/2 +TGTTGCTGCTCTGCAGGAGAGTGTGTTAGATAGATTCCTCTACCTTTGCTCAAGCCTTGTGATTATTCTGTTGAAGAACTTCAGTNN ++ +JGGIIDHHIJIGHCHGG?GHIIIE>?FCHGIGHIIJGIGIJIDHHGIIJIGIGHGIGIGEE@EHHHHHHFFFFCDFEEDDEECDEDC +@HISEQ1:121:C0EP5ACXX:8:2208:11196:39835/2 +TAATTAAGACTATGCACTCTATGAATATCACTGAAGTTCTTCAACAGAATAATCACAAGGCTTGAGAAAAGGTAGAGGAATCNNNN ++ +EF:3,<+3CCDGHG@GGGGGG9?BH4?CF@BDHEG?HE*?FGGDHHGDGICGD48FDHHIIGEHEG(7A=??7?@D@@BBACDCEA +@HISEQ1:121:C0EP5ACXX:8:1202:2784:55498/2 +TGAGATTGATTGGATCCGGAAATATGGTGTTGCGTTCAGTCTTACCGAGTATATTATAAGTAATCTCATTCCTTGTTTTCGTTGTAA ++ +IJGIFJJIIJJIJIJJJJJHIJJJJIJBFGHIJJIJHGJHHIJJJJHHH?DFFFFFEEEEFEEEEDDDEEEFDDDDDDDDDDDDDD@ +@HISEQ1:121:C0EP5ACXX:8:1308:6994:8081/2 +AGACTGTGCATGTTGGATCTCAAGATTAGATGTATTATTGGAATCAATTTTGTTGCTGCTCTGCAGGAGAGTGTGTTAGATAGATTC ++ +FF@BHEIEIJJJGG9E3FGHGGGD@>>ACC;;@;?>5;8>CCCCCC:A>C@:CCCC:@@>CC3+8???>CCCA +@HISEQ1:121:C0EP5ACXX:7:2301:2438:126170/1 +ACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGT ++ +=:EFEIIIEEBBEEFEFEFE4?DGFIECFII>GFGFIIIIFGFGFIIIIIIC;DEIFIFAB@?5=AA@BB +@HISEQ1:121:C0EP5ACXX:7:2307:15824:34753/1 +CTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACN ++ +JJJJJJJHGHJJIJGIIGGIJJIGIIJJJJJJIJIIJJIIJJJJJGDHGGGHHGIHHHFDDDDDDFDDDDDBBCCDDDDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:7:1307:10967:98956/1 +CCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCAGATCCGN ++ +JIJJIIJJIHGHIJGIJJJJJJJJJIIIJIGGHHIIJJJJJJJJIJJJJGCGHGHHGHFFFFEEECEEDDDBDBDCDDDCCCDDCD? +@HISEQ1:121:C0EP5ACXX:7:1204:2070:27164/1 +TTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTG ++ +JJJGHIJJHIJJGGIJJIFHGIIIJJJJJJJJIJJJJJFIIHHHHHFFFFFDEEEEEDEDDDDDDDEEDDCDDDDDDDDD@DDDDCB +@HISEQ1:121:C0EP5ACXX:7:2203:9357:39154/1 +CCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCTTCCTGGCCTCCTCTGCTCCCTGCGAATGGTGATTGGN ++ +J@FIIJJJJJJJIGCHIDGEHGIJGIFGIJIJJIJIJIIHHIIEG@FHIJIHGIGEHHHHFDFFEDEDEDDCDDD/=CDDDCC>AD< +@HISEQ1:121:C0EP5ACXX:7:1301:9698:5102/1 +TCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCAGATC ++ +JJJJJIJJIIIIJJJIIJIJJJJIJCHGIJJJJJJFHIJJJJJJJJJJJJJJIHHHHHEEEBEECEEEDDDCDDDDBBDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:7:1301:12379:185214/1 +TCCCTGCGAATGGTGATTGGAGATGGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGNN ++ +IHHIIFIHIJJJJ9DHHIJIHEGIIGEIDFHIIIIEHIHEFGHJJIIFHFFFFFEFDC>CC>CCCDD@CDDECDDAACCDEDDDDDC +@HISEQ1:121:C0EP5ACXX:7:1302:19292:99635/1 +CTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCAGATCCGATGCTCGGCG ++ +JJJJJJJJJJJIIJJGIJJJJGIFHIJJJJJJJJJJJIJEGIJJJJJJIJJJHEEEEEFFFFDDDBCDDDDCCCDDDBBDDCDBDBD +@HISEQ1:121:C0EP5ACXX:7:2306:17747:145219/1 +TAGAAAATAGTAAACAAACTATAGAATTGAAACAAGAGCCACACCAGGAAAGAGCCTTGATCAAATAAATCAAACCGATCTAACCT ++ +G@GIHGIGIGAEC@EEHIGGIGEFGH>GHHIIIIHIEICHGHIGIIIFCGGIIIGECEC;;?CDDFFC>CACACA?BBDD?(:AAC +@HISEQ1:121:C0EP5ACXX:7:1304:7016:24190/1 +ATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTT ++ +IJIIHIIIJJIJIIIIJIGDFEHJIHJJJJJJJJJJJGIJJHHHHHFFFFFFCDEEEDDDDCDDDDDEECCDDDDDDDDDDBEDDDD +@HISEQ1:121:C0EP5ACXX:7:2301:6715:183785/1 +CTTGAAGGAGTTTCGTTCCTCGCCTCTGTTTTCGCAAGGAGTTATGGACAACCCCCCTTCGTTGCTGGAACCACAACCCAAGGTTAG ++ +JJJJJJJJIJGHJJJJJIIIIIJJIJJIHIJJIJJJIJHFHHFFFFFDEEDDDDDDDDDDDDDDDDDDDDDDBDDDDDDD?BD>CCA +@HISEQ1:121:C0EP5ACXX:7:1203:2790:175160/1 +TCGGCGACCTAAAGAGACTGTATTCTTCAGCAACAATCAGATCCCCAGATTGATTTGCTCTGATGGCCGCTCTTGAAGGAGTTTCGT ++ +IIIJIJJJFJJJJJGIDGHIJIGIDIIFHJGGGGGIIJGDHHHHFFFDDEEECDDCCDCDDCCDDDDDBDDBBDCDDD<@CCC>CC@C;ADDDD@:8 +@HISEQ1:121:C0EP5ACXX:7:1102:17294:172346/1 +ATAATACATCTAATCTTGAGATCCAACATGCACAGTCTCAACTGGAAAGGATCAATTCTAACTAGATTAGAATAAGCCAGGGAAACN ++ +JJJJJJJIJIJJJJJJJJIGIJJJJJJJJJIJJJJJJJJJGIJJJJJIJHIJJJIIIJJJJIIJJFHHHHHFFFFFFCEDDBDDDCA +@HISEQ1:121:C0EP5ACXX:7:1208:9741:160200/1 +TGCTGGAACCACAACCCAAGGTTAGATCGGTTTGATTTATTTGATCAAGGCTCTTTCCTGGTGTGGCTCTTGTTTCAATTCTATAGT ++ +9A@H(..=3?C:);;.)7?@>;>A>AC@C@C(5((5,59@C:@(:(4(::4:@4>3:B +@HISEQ1:121:C0EP5ACXX:7:1304:10851:86218/1 +CGTTGTAAGATTAGTTATGTTTCCCTGGCTTATTCTAATCTAGTTAGAATTGATCCTTTCCAGTTGAGACTGTGCATGTTGGATCTC ++ +EHBEAHGGEFHGB@EDDG@?FEGIIGGGGGCHGIBGIGHGEACA +@HISEQ1:121:C0EP5ACXX:7:2204:19880:81834/1 +AGGAAAATACTTTATCAAAGTCATAATTAAGACTATGCACTCTATGAATATCACTGAAGTTCTTCAACAGAATAATCACAAGGCTTG ++ +JJJJJJJJJJJJJIJJJIIJGGGJIJJJJJIJIJJJJIJJIJJJJJJJJJJJJJIIIBFGHIFHJJJJJJHHHHHGFFFFDECCCEB +@HISEQ1:121:C0EP5ACXX:7:2303:19926:13623/1 +GAATACCAACTCCCCAAATTTACCAAATCTCACACCACCTTGTGGTAGCACAAAAAGTTCCAAACCAAAAGTGACCAAATCAGGTAC ++ +IJJIJJGIJJJJJJJJIJJJJJJIJJJJJGIJHIJEHIIJJJIIICGIHHHHHFFFF@CDEDCEDDDDDDDACDDDDDDDDDDD>CC +@HISEQ1:121:C0EP5ACXX:7:2306:15928:63590/1 +AAAATAGTACGACCAACATCAATGATGCTTACCAACAAAACAAGGGGAATACCAACTCCCCAAATTTACCAAATCTCACACCACCTT ++ +IIGHIGBAFHHGGIIIEDD@DG@@@GGEEGIIGHGIGGHGIIGGCAHHFFEE3@DDAC@ABA;ACCCCDCCCBCCC>ACCCBBBBA@ +@HISEQ1:121:C0EP5ACXX:7:2105:7681:133379/1 +GTACTATTTTTGGTAGCATCATTAATCACCATATCAGCAAAGGAAAGCTTCCCCTTCCCCTTATCCATAGCAACCCTCTCTTCAGTN ++ +JJJJJJFIJJJGICGGGIJGJEIIJJJJJJJJJJIIIIIJJJIJJIIIJJIJJJJHHHHHFFFFFECEEEEDCDDBDDDDDCDDCBA +@HISEQ1:121:C0EP5ACXX:7:2102:2292:138014/1 +CATTAATCACCATATCAGCAAAGGAAAGCTTCCCCTTCCCCTTATCCATAGCAACCCTCTCTTCAGTAAATGCACACACCCACTCAC ++ +JJJJJJJJIJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJIIHHHHHFDFFFFEEDEEDEDDDDDDDDDDDDC +@HISEQ1:121:C0EP5ACXX:7:1307:11840:86884/1 +TTTGCTTGGGTTCTAGCAAGAGCAAGTTTATTAAAGAGAGCTTTGGGATCAAAAGTTTTGGTACCTGATTTGGTCACTTTTGGTTTG ++ +JJIIJJJIJJFHGHIJJJJIGIIJJJJIJHJJJJJJJIGHHHFFFFDDEDEDDDDCDEDDDBCDCDDDDDEDCBDDDDDDDDCDDDD +@HISEQ1:121:C0EP5ACXX:7:2207:1406:103949/1 +AACCCTCTCTTCAGTAAATGCACACACCCACTCACTGTATCTAAAGCTCACTATGAATATTAACCAGTACAGAGCAGATTTACTCGG ++ +JJJJJJJJJJJJIJIGJJJJJJIJJJJJJJJJIJJJJHIJJJIJIJJJJJJJJJJIIJJJJHHHEGFDFFFFEEDDEDDDDDEDDDD diff -r 000000000000 -r 05c27700e5ca demo_files/father_2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/demo_files/father_2.fastq Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,132 @@ +@HISEQ1:121:C0EP5ACXX:7:1203:4036:101367/2 +AGAAAGGAAAGAAAACAAGCACAGAGGGGAGGAGCAAAAGCTCCATCCTAGGCTTGGAAGAGATTCGAACAAGAACAGAGAAGAANN ++ +IIJJJIJJJJJJIJJIJJJJJJJJJJIJJJJJJJJJGHIJHHHHHFFFFFFEEEEDDCDDDDDCDDDEBDBCCDDDDDDDDCDDD?> +@HISEQ1:121:C0EP5ACXX:7:1104:4621:84657/2 +TAGGATGGAGCTTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTN ++ +JJJJJJJJJJJJJJJJJIIIJJJJJIJJJHIJJJJFGHIJJJJJJJJJJJJJJJJJIJJHHHHHFFFFDCEEEDCDCCFECDDCCDD +@HISEQ1:121:C0EP5ACXX:7:2302:14544:194571/2 +GCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTN ++ +JIJJJJIJJJJJJIJJJJJJJJJJJIJJJJIJJHHHHFFFFEEDDDDDDDDDDDDDDDDDDDDEEDDDEED>CCDDD8?BDDCCCD@ +@HISEQ1:121:C0EP5ACXX:7:2104:2793:10052/2 +ATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTT ++ +DEH93CDG>78?:CGHAGHHEGHIIIJIIIJGIIJIIJHIJHHHEHDFFFFFDEECEDDEDDDDDDDEEDDDDDDDDDDDD@DCBCC +@HISEQ1:121:C0EP5ACXX:7:1305:17112:135146/2 +CATCTCCAATCACCATTCGCAGGGAGCAGAGGAGGCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAANNNNNNNNN ++ ++22E>@DFCDEDDDDDBBDDDDDDDDDDDBD1?BB9CEHDHEFFFFFDEDCADD@AC3>@ACDDC +@HISEQ1:121:C0EP5ACXX:7:1106:19675:197765/2 +CGAAAGAGAGGCAATAATTGTAAAGTAAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCN ++ +JJJJJJGIIIJJJJJJJJJJHIJJJGHIJJJJJJJJIJJJJJJJJJJJJJHHHHHHFFFFFDEDEEDDDDDDDDCDDEDDDDDDDEC +@HISEQ1:121:C0EP5ACXX:7:1102:8367:114087/2 +CTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGAAGACTCCAAATAAGAGGCAAGTGAAGAGATTC ++ +?CGGEFG?:C?AG8@@3=>8BCFCG@D@4@DEA=7A<,;CE>C@>(.--55;>>CCCCA:C@???2<+43:::2?@@C +@HISEQ1:121:C0EP5ACXX:7:2102:5258:155716/2 +ACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGGCCTCC ++ +3CFFHIGGIJGHGIHGGHH5@CDDDDDDACCCB:9>@>>@@>(944::A>A>33:@C>C@AB +@HISEQ1:121:C0EP5ACXX:7:2307:15824:34753/2 +ACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAA ++ +JJJJIJJIJJJJIJIJIJJJIJJJIJJJFGIJJHIHEIHJHHF>?BDDDEDDDDDDDDDDEECDEDDDDCDDCCDCCCCCDCDDCD +@HISEQ1:121:C0EP5ACXX:7:1307:10967:98956/2 +AGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTC ++ +JJJJJJJJIIJJJJJGIIF@GHIJJIJIJJJIIIJJHHDGHIGHHHFD>BDCDCEDDDDDDDDDDEEDDECDDDDDCDDCACCDDDC +@HISEQ1:121:C0EP5ACXX:7:1204:2070:27164/2 +GAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGANN ++ +IJJJJJIJJIIJJIJJIJJJJJJJJJJJJJJIJIJIIIIHIJIJJHHHHGFFFFFCCCEEEEEDC@CDDBDBB@DCDDDBB>CDAC< +@HISEQ1:121:C0EP5ACXX:7:2203:9357:39154/2 +AGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGNNNNNNNN ++ +GGIIBHDGGIGG@FIIJJIJJJIGIJJJJIIJIJJIIIIJIEIIHHHHHFFDFFFDEEDEEEDDDDDDDDDDDDDDDDDDACDDDDDDC>A@C +@HISEQ1:121:C0EP5ACXX:7:1302:19292:99635/2 +AACTATAGAATTGAAACAAGAGCCACACCAGGAAAGAGCCTTGATCAAATAAATCAAACCGATCTAACCTTGGGTTGTGGTTCCAGC ++ +JJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJGGIJIJJJJJJJJJJJIJJJJJJJJHHHHFDDEDDDDDDDDDDDD@DDCBDDDCC +@HISEQ1:121:C0EP5ACXX:7:2306:17747:145219/2 +GGCCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATGGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAN ++ +3C>ACDGECHGG>BGGIJJI?DC?@CCCCCCCDC@C +@HISEQ1:121:C0EP5ACXX:7:1304:7016:24190/2 +AACGCAACACCATATTTCCGGATCCAATCAATCTCAAACCATGAGCGACAATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGC ++ +JJJJGGJJJJJJIIJJJGJJJJEBHIIIIJIGJJJIJJJJJJJJJHHHFBACEDD>CDDDECDACDDDDDCDDDDDDDDDEDACDD@ +@HISEQ1:121:C0EP5ACXX:7:2301:6715:183785/2 +TACAACGAAAACAAGGAATGAGATTACTTATAATATACTCGGTAAGACTGAACGCAACACCATATTTCCGGATCCAATCAATCTCAA ++ +JJJJIJIJJJJJJJJIIJJJJJIJJJJJJJJJJJJJJJJJJJIIJJJJJJJJJJHHFFFDDDEEDEEEDDDDDDDDDDDDCDDDDDD +@HISEQ1:121:C0EP5ACXX:7:1203:2790:175160/2 +ATCTTACAACGAAAACAAGGAATGAGATTACTTATAATATACTCGGTAAGACTGAACGCAACACCATATTTCCGGATCCAATCNNNN ++ +IIHGCJIJJJGIIJJIGJJJDIIJJIGJDIEHIIIIGIIHEHFGHCFH@F>BDDDDCCDECCCBBD>B? +@HISEQ1:121:C0EP5ACXX:7:1102:17294:172346/2 +AGATCCCCAGATTGATTTGCTCTGATGGCCGCTCTTGAAGGAGTTTCGTTCCTCGCCTCTGTTTTCGCAAGGAGTTATGGACAACCC ++ +HHIJJJJJJIJJJJIJJJJJJJJIIJJIJJJJJJJJGIJJIHICGHHGJHHHHHFFDDDDDDDDDDDDBDDDABE:A>EHHC(7;@@@>=36@>C:?;>C +@HISEQ1:121:C0EP5ACXX:7:1304:10851:86218/2 +ATCACTGAAGTTCTTCAACAGAATAATCACAAGGCTTGAGCAAAGGTAGAGGAATCTATCTAACACACTCTCCTGCAGAGCAGCAAC ++ +GIIIIJJIIECHFHGGGGHIHHGIIJGFEHFHFFDECACEECCCCACCDDDDD +@HISEQ1:121:C0EP5ACXX:7:2204:19880:81834/2 +GATCTCAAGATTAGATGTATTATTGGAATCAATTTTGTTGCTGCTCTGCAGGAGAGTGTGTTAGATAGATTCCTCTACCTTTGCTCA ++ +JGIIIJJJIGIJGJGGIHHIIJJJJJIJJIJGIJJJHHIIJIJJJJJJJIIJHGCG=F@CDHIJFHHHHHHFFFFFDEECEEEDDDD +@HISEQ1:121:C0EP5ACXX:7:2303:19926:13623/2 +GGAAATAGACTCATGGCTAGGATCGAAACCCGAGTGCCATTGCTTAAGGAGTAAGAGTTGGCTAAATATATGGTAGGGCCTAGNNNN ++ +IJJIIJIGIJJJJIFJJJJGIECH>GIIGIJIGA7CCFFHIGHGIGIJIHH>EE:;@7;BEAACECCACDDCA5>@BDCB?AC@>:A +@HISEQ1:121:C0EP5ACXX:7:2306:15928:63590/2 +GAGCAAGTTTATTAAAGAGAGCTTTGGGATCAAAAGTTTTGGTACCTGATTTGGTCACTTTTGGTTTGGAACTTTTTGTGCTACCAC ++ +JIJJJGHHHIIIIIJJIJIHJJJIJIIIIIJIIGIHJIIIHGGIIJJJGIJJGIJJGGHHHHFFEFEDDEDDDDDDDDDDDDACCCC +@HISEQ1:121:C0EP5ACXX:7:2105:7681:133379/2 +TATCAACTAGGTGGTCTTCTTTACCTTTTGTACTCTGACTTAGCTAACTCTTCCAACAGTAGCAAAGCTTACCCCTATTTATATAAC ++ +JJJJJJJJJJFBGHHGIJIJJJIJJJJJJJIIJJJJIJJJIJIIIIJJIJJIHJJJJJIHIGEIGGHEFHFDFFFDDDEEFEEEEE: +@HISEQ1:121:C0EP5ACXX:7:2102:2292:138014/2 +TATCAAACCCCTGATCTGTCTGAGGCTGTGTCCTGTCTGAATGTTGTTAACGTGAATTGCTATACTAAGTTGCTGAACTATCAACTA ++ +JIJJJJJJJJJJIIIIJJJJJJIJJJJJIJIJJJJIGHIJJJIHIJJIGIJIHJIIJIJHHHHHHHFFFFFFFEECCEEDDDDDDDA +@HISEQ1:121:C0EP5ACXX:7:1307:11840:86884/2 +ATTCATAGTGAGCTTTAGATACAGTGAGTGGGTGTGTGCATTTACTGAAGAGAGGGTTGCTATGGATAAGGGGAAGGGGAAGCTTTC ++ +IJJIJJJIHIIJJJJJJJJJJJJJGIJJGIJJDGHIJJJJJJJIJJJIIJIJGIJJIJHHHHHFFFFFFDEEDDDDDDDDBDDDDDD +@HISEQ1:121:C0EP5ACXX:7:2207:1406:103949/2 +TCTGTCTGAGGCTGTGTCCTGTCTGAATGTTGTTAACGTGAATTGCTATACTAAGTTGCTGAACTATCAACTAGGTGGTCTTCTTTA ++ +GIIIEDHIIIIGCHEEFGGGIFHIJGGHIJJIHHJIHHHIJGIJIIJGIIJIGIIHIIIIHHHFHHFFFFFFEEE>@B?CCDDDDDC diff -r 000000000000 -r 05c27700e5ca demo_files/father_male.bam Binary file demo_files/father_male.bam has changed diff -r 000000000000 -r 05c27700e5ca demo_files/father_male.bam.bai Binary file demo_files/father_male.bam.bai has changed diff -r 000000000000 -r 05c27700e5ca demo_files/mother.bam Binary file demo_files/mother.bam has changed diff -r 000000000000 -r 05c27700e5ca demo_files/mother.bam.bai Binary file demo_files/mother.bam.bai has changed diff -r 000000000000 -r 05c27700e5ca demo_files/mother_1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/demo_files/mother_1.fastq Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,704 @@ +@HISEQ1:121:C0EP5ACXX:8:2204:19496:144054/1 +GGCGAATCCCCACAATTTGCAAGGGCAAATTATGTGTTCCACCACAAAATGAAACAAGAAAGGAAAGAAAACAAGCACAGAGGGGAG ++ +GHFHGHJGDHGGG=@DGHGIGCDHFHAB@DEFFCFFECECCCDDBBADDDDCDDDCBCD?A:?ACCACDD3?ADCDDCDDCCB@><< +@HISEQ1:121:C0EP5ACXX:8:2204:8525:81513/1 +ATGGGTAAAGTTTTGGGTATACGGGGCGAATCCCCACAATTTGCAAGGGCAAATTATGTGTTCCACCACAAAATGAAACAAGANNNN ++ +IJJJJCIIJJJJJJJJJCEHGIIJJIIJIJHHHFFFFDDEEEDDEDDDDDDDDDDDEDEEDCDDEDDDDDDBDDDDDDDDDCCDDDB +@HISEQ1:121:C0EP5ACXX:8:1103:3495:189629/1 +CCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTG ++ +GHGIGIGII>>HH@FGHIGGCGGGIIIIIIEBFGHIGHIGFHHICHCHIGDFGGIIIGEAEECEFFFCCCEECCCDCCACDDDCDC@ +@HISEQ1:121:C0EP5ACXX:8:1304:11225:78484/1 +CTCTAAAACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCT ++ +GG@CFHGIIFEF<9EG@FCD?FGGEBFGHGB@BDHGEGHICGGHIIIEEHICGGH@DHE@CE>A>CE@3;@A>?ACCC;ACC@??<< +@HISEQ1:121:C0EP5ACXX:8:1108:5040:99148/1 +TCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTCCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATT ++ +JJJJIJEGJJIJIJGGJIHGIJICHJIIIIIIIIIJJJFIIJJJJJIIJJJJIJIEECEHGFHFFFFFEE@CAEEDDDCCCDDDDDE +@HISEQ1:121:C0EP5ACXX:8:2205:18768:173013/1 +TCCTCTAAAACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAG ++ +HIIFIJJFGIIJIJGGAGHIGIGIIIIIIDDDCFIHGHGGIJIJIIGIIJJJIJIIGACGHAEHFDFFFFFFEACDDCACCCACDC@ +@HISEQ1:121:C0EP5ACXX:8:2304:9392:61526/1 +TACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTT ++ +JJJJJJJJIJJIHIGHIJIJJJJJJJIIIJJIIJJJGIIJJJJJIIHJJJJJGIIJJJJIJJFHHHHFFFFFEDDCDDCCCCDDD<@ +@HISEQ1:121:C0EP5ACXX:8:1107:8798:32463/1 +TCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTAT ++ +JJJJHIIIIIIJJJJJJJGIIJJJJIIIJIGEHIIJJHIJIIIIJJJJFHIIIJJIIJJHHEHFDDDFFEFDDDBBCDDDDDDB5FIIFEFFF.=)7=>;>B@.6>A(6;>@5>@;5>? +@HISEQ1:121:C0EP5ACXX:8:2304:6536:185404/1 +GAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCCCCACAATTTGCAAGGGCANN ++ +JHIJJIJJJJJJJIJJJJFHIJJJBFHJJGHGHIJJJJJBFHGIGHJJJJJDEFHHHHFFDBDDDDDDDCBDDDDDDDEDDDDDDDB +@HISEQ1:121:C0EP5ACXX:8:2305:5708:181701/1 +CCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTG ++ +BGGIEGGIGGGIIBFGGCE>>DC?CFGHIGGHIGFEHEIIIIII;==CEAAHEEDAGGH?EHBCDFFBBCACCCCCCAA=?B@A@A> +@HISEQ1:121:C0EP5ACXX:8:1206:13113:50926/1 +GAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCCCCACAATTTGCAAGGGCAN ++ +B+A:CFI;9+:9?:CEE9C9?D<;):B88>>>A>>(:<FHFCGHEGGHGHICG@DD?9B>=FGIGA@DHGII;CH??>B>;>C@66>C>A=CC?@CCC +@HISEQ1:121:C0EP5ACXX:8:2105:21271:167682/1 +AAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTT ++ +IICIGJJIIGGIGGJFIJI@GGHIJIIJJGHGGHEIJJI;FHIGH:C@FIJGGEG47B;?CCHHE@B97>?ACCABD=CCC:BA +@HISEQ1:121:C0EP5ACXX:8:1302:11743:35278/1 +GGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCNN ++ +ACFEEF+?F9BBHD@BFFH??FGIFHFFCDE@>?DFHG;)).).=CH@AEHHBE;7>>CAC;>;;>>;5>>C?3@@ +@HISEQ1:121:C0EP5ACXX:8:1307:11530:167684/1 +CCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTG ++ +IGAFHGCIIBEEFFGHE>CFHI@E@EHGIGIGEH?DFDHGHIIE=CAEHIIIIHIIEBHEA7=;;;?;AC@AC>5>>A?CCDBCBCC +@HISEQ1:121:C0EP5ACXX:8:2306:2962:37980/1 +TGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGAAAAGTTTTGGGTATACGGGGCGAATCC ++ +E3;1;;)CEFEDECEDA=DCDA>DDIDC>B=BBBCCEACEEDA2.=@D>=C7=;;@DDD3>>A>@AAA=?:?AAD>?A +@HISEQ1:121:C0EP5ACXX:8:2307:9346:102436/1 +TGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCC ++ +GJJIHEHGGGGIJIIBHEEBF@FGEIIICHGHIBDHGI@=CFHI(@CGE=CAEHHFF@D);;@A@CEDB@@?C@ACABBB>CCCCDEDDDD8@CDDDBDDBDD@5 +@HISEQ1:121:C0EP5ACXX:8:1203:20081:59684/1 +ATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACN ++ +JJJJJIJIJJJIJJJJJJIJJJHIJJJJFIJIIIJJJJJJJIHHIIJIGIJJGJIIH;CEHHFFFFFFCCDFEEECD???BBDDDD? +@HISEQ1:121:C0EP5ACXX:8:2202:6060:140689/1 +TTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATNNNN ++ +JJJJIJJJJIIJJJJJJJJJJJJEIGGHGHIIIGIIJHIJJJIGGHIIIJJIIJJIHHHFECDCDDFFF:@C?@?BBCCDDBDDCDD +@HISEQ1:121:C0EP5ACXX:8:2206:18846:173028/1 +CCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGNNN ++ +JJJIIIEGHIJIJGIIIJJIGDGFHHIIEGFGIIJFFAEEDGGHGECHEEEBD@CB@CEDCAACCDDDEDDDDBCCADBDDDBDDB> +@HISEQ1:121:C0EP5ACXX:8:1205:18182:73982/1 +AGAACCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGC ++ +JJJJJJJJJJIJJJJJJJJJJJJJJJJIIJIJJJJJJJJHHHHHEHHHFFBDDCEDEEFDCCDDDACCDDBCEDDDD<@CDDDDDD< +@HISEQ1:121:C0EP5ACXX:8:1206:1811:22216/1 +TCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCC ++ +;EG9CCE@>H@FBDGGEE?D<B4=C5>5;;>@ACCCB +@HISEQ1:121:C0EP5ACXX:8:2307:19323:17727/1 +GGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGCACACATAATTTGCCCTTGCNN ++ +JJJJJJIJJIJJJIJJJJJJJJJJIJHIIJJJGHIJJJJIJJJJJIJJJIIJJJIJJJGHHGHDFFFEEEDEDCDEECDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:2304:13953:99797/1 +GGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCNN ++ +FG@4<@G@>CGGCEBEED9?CCGG>GGIIGIEFDDAHIII=FHHGGGFC@FGEHGCHI;?>AED?DECCC?CCCCDE<>55>CCCC> +@HISEQ1:121:C0EP5ACXX:8:1206:2780:83786/1 +TCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTG ++ +AFEDHFGIHICEAGGG=CC=DE=;?CEEEEE>?C@3@CCCCCCCDEEDC?? +@HISEQ1:121:C0EP5ACXX:8:1302:14767:71234/1 +TCCTCTAAAACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAG ++ +JJJJJJIJJJHGIJJJJJJJIJIIJIJIJJJIJJJIIJIJJJGJIJJJGIIJIJJJJGIIJHGHHFFFFFFFEDEDDDDDDDDD?AB +@HISEQ1:121:C0EP5ACXX:8:2103:4557:157261/1 +GGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCNN ++ +H@F:CFGHHHIIGGGIGIIIIIBGGIBGHGGIFHEIIEHHEDFGHHIG=@FIDDEHGGHEE=??BEFEEECECCCDC:>@CCCCCCC +@HISEQ1:121:C0EP5ACXX:8:2302:4919:198649/1 +CTCTCCTCTAAAACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGNNNN ++ +JJIJJJJJJJJJJIIJJJIJIIJJJJJIJJIJIJIJJJJJJJJJJJJJIIJJJJIAHGIIIJHHFEDFFFFFECECEEDDDDDDDDC +@HISEQ1:121:C0EP5ACXX:8:2102:15481:17585/1 +CAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCGAGCACCGATCTGAGAACCTGGGAGCAAAAATCGAAAGAGAGGCN ++ +JJJJJIIJJIJJCHHIIIFIFJJJIJJJIIJJJJIIGIAGHEHFFCDEDBBBBDDDDCDDDCBDDDDDDCCCDBCDDDDB>CCBBBD +@HISEQ1:121:C0EP5ACXX:8:1102:3776:50474/1 +ATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAAAATCGAAAGAG ++ +IJJJJJIJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHHHFFFFDDEEDDDDDDDDCDDDDDDDDBDDBDCDBDCBDDD>A9 +@HISEQ1:121:C0EP5ACXX:8:1106:16133:150529/1 +ATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAAAATCGAAAGAG ++ +JJJIIJJJJIGIJJJIIGIDIGIIJJJGJJIIIJGJIIJIJJHHHFFFFEDBEDDDDDDD>@CDCBDDDBBDDDDDDDBCDDDDBDC +@HISEQ1:121:C0EP5ACXX:8:2306:7300:185913/1 +CTAAAACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTT ++ +IGIJJJJIHIJJIHGIGI>GHGIJJ>GDCIIJIJJJJJJIJJIJJJJJJJIJJJIIIIEGHEHHHFFFFFFDDCCCDDCDDDDCDDA +@HISEQ1:121:C0EP5ACXX:8:1201:6936:191697/1 +TTCAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAANNN ++ +JJJJJJJIJJIIJJJJIAEHIJIIJIJJIJIJJJJJJIJJJIIJJHHHGFFCCCDBBBDDDDDDDDDCCCDDDDDDD@ADDD?CDD< +@HISEQ1:121:C0EP5ACXX:8:1103:1745:180624/1 +CTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGC ++ +JJJJJIJJIJIJJJJJJFEHGIIGIJIHDCCFHHEHHHIIJCDHIIJIJIIIJIGHIJEHHE>EDDFFEEECDEDDDDBBCBCC@>> +@HISEQ1:121:C0EP5ACXX:8:1206:17568:25304/1 +TGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTATACCCAANN ++ +EHGEHGIIGFHGGHJFGEGEGHEGIHIJIAFH?BFHGIIHJIICGIIGGIHH9FGGGDGGHCAHBBC>A;?BB?BB89>CC:@DFC>CBCD?BCAGFFFCGIICFFEC9BFFFDFF)*=C@:AB@;;;;;=@98@B=@<8?@@<@@B5>@BDDDBDDDBDDDDBDDDBDDDDDB +@HISEQ1:121:C0EP5ACXX:8:1201:10878:193365/1 +AGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTTCAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGNN ++ +JIJJJIIIJFHIIIGEGIJJJJG?GHGIJJFHGJJJJJJJJJGIJJJJJIIGCHHHHHHHFEDDDBDDDDDDDDBDDDDDBDDDDD8 +@HISEQ1:121:C0EP5ACXX:8:1107:3570:34778/1 +TCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTTCAATCAATCTCCAATCACCATTCGCAGGGAG ++ +JJJJIGJHHHGICHIJJJIJJHGIGIJJJHHIIIIJIJJIIJJ@@GHIGIIJJHFHHHBEFCFFEEDCEEDCDDDDDDEDDDDDBDB +@HISEQ1:121:C0EP5ACXX:8:1104:15089:78984/1 +CTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCTGGTGAGAGCAGCCTTCGATCCATCTCCAATCACCATTCGCAGGG ++ +JJJJJIJJJIGAEHIJJJIIIJIGIJJJIIJGHIJJJJJJJJJJJ=CFHGGIJIIHHHHHFEFFEEEEEDEC>CCCDDDDDDDDDBD +@HISEQ1:121:C0EP5ACXX:8:1101:10457:23604/1 +GCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTATACCCN ++ +IJJJJHJJJJJIJIIJJJGIJGHIIGIIJJJGIJIIIIGJJJIJJJJJJJIJJJIJIGFHFEHHHFFFDDDDDDDDDDD>>BDDDDC +@HISEQ1:121:C0EP5ACXX:8:2305:17031:5327/1 +ATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTT ++ +CBBDF:C@EFE@*?1DDD6?:D@DDE@CCDACAACCDIACDCCD;;7;@@?@=AAAAAAA>>>AAAAAB3>A>>>>>AAA?>>A?>> +@HISEQ1:121:C0EP5ACXX:8:2102:21212:46392/1 +TCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTTCAATCAATCTCCAATCACC ++ +JJJFIIIJIJJFIJJJJJG>FGHJGEIIJJEGIHIIJIJIJ4CGIJIJIGHIJIJ:=CDCFEFEEACCDDDDDCD>@CDCDCCDCDC +@HISEQ1:121:C0EP5ACXX:8:2102:10309:35842/1 +TACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCC ++ +JJJJJIJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJHHFHFFFFFFEEEEDDDDDDDDDDDDDC +@HISEQ1:121:C0EP5ACXX:8:2203:18766:43466/1 +GGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCNN ++ +JJJJJJIJJJJJIJJJJJJJJJJJJJFIIJJIHIJJJJIJIIIJJJJJJJIIJIIIIIIHHGHFEEFEEDDEDDDEEDDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:1308:4675:83154/1 +CTCTCTCTTCTTCTCTGTTCTGGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGGGCTTGTTTTCTTTCCT ++ +IHHGEEHICFGG@CFHGFHGH+?CBFII)?GFHIIIGDB??FBHF9C)=B@=8@7=CGGCGEEHFDDBCC(;A=ABB:CCCCCCCCC +@HISEQ1:121:C0EP5ACXX:8:1107:5242:86751/1 +GCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTC ++ +JJJJJJJJIJJJJJJJJJJIJJJJJJJJJJIJJJJJJJJIJIJJJJJJJJJHIIIIIJFHEEHFGFFFFCEEEDCBDDDDDDDDCCC +@HISEQ1:121:C0EP5ACXX:8:1306:15890:88846/1 +TTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTC ++ +IJJJJIICGHIJJIGIIBEHIIJJGIJJJGGDGHHIJJGJIJJJJJIIJJIJJIJJJEGHHEEHFFFFFEEDDEC@@5;=CCC@DDC +@HISEQ1:121:C0EP5ACXX:8:2103:4321:176641/1 +GAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCN ++ +JIIHIHHIIJJ@FHGHIJGIDHDHGIJEHGIJGHIFGHHGFFFCEFDEEEEDC@CDDDDDD@BDDCDDEDDDDCDDDCB9GGHGEAGEGIDGBHDGIGII4@E=C7?CFFFECBCCCCDDDCD??CCCCDDD>ACDCCD@CCC>>CCCDBBB?B@>CD@A<9@CD +@HISEQ1:121:C0EP5ACXX:8:1303:12868:89901/1 +TTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTT ++ +JGCGIIJJIJIJIIJ@HGGCBGIIIDFGHICHEHIJIJC@FGEHJHJJIJJJIGIEGHIBHHHGCEEDDDDAA@@CC;AA@CDDCDD +@HISEQ1:121:C0EP5ACXX:8:2105:10194:4856/1 +AAACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCT ++ +JJIIIJJIJJJJJJJGIAGGIIJJGJJIHIJIJGGIIJJJJJJJFHIGGIGGEHICEHEEEEHHGFFDDFC@CEC>@BCBDDDDC>@ +@HISEQ1:121:C0EP5ACXX:8:2303:17380:176758/1 +AACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTC ++ +JJIIIJJJJJIJGIJIJIIEIJJFGIIJIJIGIJJJIJJJJIJJGIJJJJJJJI?@EHIGHEHFHFFFFEEEEECDDDDDDDCCCDC +@HISEQ1:121:C0EP5ACXX:8:1301:11188:179944/1 +GGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCANNNN ++ +JJBHIJJJJIIJJJJJHIIJJGGBGGIJJJJ:@ECECEDEDDDDDDDDEEDDEDDDDDDDDCCCCDDDDDDDCDDDDCCDDDDB<>> +@HISEQ1:121:C0EP5ACXX:8:2306:14700:199855/1 +CATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAG ++ +D;C@CC?;?83(:@AC>:55:::C>>4>@>A>@3:@@<8? +@HISEQ1:121:C0EP5ACXX:8:1105:6834:23521/1 +CTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGG ++ +JGGGHIIIJEIJJJJJJJIFJJJJJJJDFHIJJJJJHIJJJEGCHIGHIFHHHHFFFFECDDDDDDDEDDEDDCDDDDDDDDDEEDD +@HISEQ1:121:C0EP5ACXX:8:1304:15370:31007/1 +CTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAG ++ +FGHGICH@HHIG@BGEI=FFCBC=@GHIEGH=A??@5@CCCBCB?CC@@@><@C@BCC@AACCCCC:ACCCC>CCC>>>C +@HISEQ1:121:C0EP5ACXX:8:1302:2247:98264/1 +AATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCN ++ +JJJJJIJHJJJJJJJJIEFGGHIGIJJJJJJCHIJJ@GEHJIHHHF8>@CCCDDDDDCDDDDDEEDDDDDDDDDCCCDCCDDDDDDC +@HISEQ1:121:C0EP5ACXX:8:2306:3485:63749/1 +GCCCTTGCAAATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCT ++ +JJJJJJJIJJJJIJEHJJJIJJJJJJJJIFHIJJJJJJJGJHHHHHHFFFFFFEEDDEDDDDDDDDDDDEDDDDDDDEEDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:2208:8405:84311/1 +CCTGGGCTCCTCTGCTCCCTGCGCATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTG ++ +GGHIEHIIGJJJIIJGIJJEIJI)?FHIFHGHIJEGJGIIJCHIGIAGHHHHEFFFFDFEDBBB@>CCDDDACCDDDDDDDDDCEED +@HISEQ1:121:C0EP5ACXX:8:2302:12851:12461/1 +AGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTC ++ +IIGIGHGI>CGHGHHGGIIHGBECEHFCB8;:A@CCCCB9A??@CDDCB>ABBD>CCCDD@>:AACC +@HISEQ1:121:C0EP5ACXX:8:1305:5063:120920/1 +ACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGT ++ +JJIJJJJJIGIIJJJGHIIGIIJJIJJJIJJIJJIJIJJFGEIJJJJJJJJIFHIJJJHHHHHFFFFEEEDDECCDDBBBDDDCCBD +@HISEQ1:121:C0EP5ACXX:8:2105:14420:64218/1 +TTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTC ++ +GGGIIJJHIIGIJGHIJGGGHGHIDEGIJEHIGEGHGIGGA@DGHIIJIJ?HGHFCB@EHEACEDFFDECEEEE@=@=?=ACC<>AC +@HISEQ1:121:C0EP5ACXX:8:1106:15317:167117/1 +GTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCN ++ +JJJJJJJJJJJJIIJIJIIIJJJJJIJGHIJJJJJJJJJJHEHFFFFFEEDEECBD;>BCCDDCDDDDDDDDDEEDDDDDDDDDCD> +@HISEQ1:121:C0EP5ACXX:8:2205:12047:48476/1 +ATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTG ++ +IIJJEGGIIJJGIJJJJJGJGIIEIJIJIIJHGJJJGIJIIJIIJJJJIEHIJJJJJJHHHFFHFBEFFDDDDDDDBDDDDDDDDCD +@HISEQ1:121:C0EP5ACXX:8:1307:16680:41377/1 +CTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGNNNN ++ +JIJJJJHJJIJJGIIJJIIIJDHGFHIJGGIGEFFHIIIIHIIJJJJJGIJGHHHHFFDFFEEEDEEDDBDDDC>CDDDDDDDCDDA +@HISEQ1:121:C0EP5ACXX:8:1301:3542:41315/1 +ACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGT ++ +JJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJIIJJJJJJJJJJIJJJJJHHHHHFFFFCCEEEEEDDDD?<@BCDDBD +@HISEQ1:121:C0EP5ACXX:8:2202:5040:37535/1 +TACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGNN ++ +JIIIJJJJJJJIIFIIJJJIJIFHIJJJJHHIGIJIJGHJJJJJIJJIJDFHIIJHHHHEFDDDDCEDDDDDCDD@CDDDDDDDDB> +@HISEQ1:121:C0EP5ACXX:8:1301:20965:126815/1 +TTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCN ++ +IJJIIIJIJJJJJJJJIFGGBHIJJGIIIGIJJGIGIJJJIIIHIIIJIJJGIGCEEECFEBBDBBDCDCDDDDDDCCCDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:2208:7542:56931/1 +CTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTN ++ +HIIGIIIIIIIH9CHHE>FGGCGIGIIIFEIGIIIEHHICGIEHIIIIIIGIIIGIHHFD?>CCEEC@CCCB=?BBCCBB@B9@@BC +@HISEQ1:121:C0EP5ACXX:8:1108:16683:76874/1 +AGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGN ++ +JJJJJJJJJJIGIJJJJJIIIJJJIJJJJJJJJJJJJIJJJJIIHIHHHHHEHFDEFDDDD@BDDDDDDDDDDDDCCCCDDDD<C@CBCCC?C> +@HISEQ1:121:C0EP5ACXX:8:2106:16519:145675/1 +GGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAG ++ +JJJIJJJIJHGIIJJJIIFIGIIJJBFHIJJJJIIGHGIJJIIJIJJJJHHGHHDFFFDDDDDDDEDDEDDDDDDDDDDDDEEED@C +@HISEQ1:121:C0EP5ACXX:8:1201:11309:101312/1 +AAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTG ++ +JJIJJIJJIJJJIIIGIEHGIGIJJJJJJJIJIBHIGGGGIJIHHHHGGFFEFFFEDEEECCCDDDDD3=??@><<@CC@DGI>CDE?DFDFGFFCBDDBB>;8????@>50+25AA +@HISEQ1:121:C0EP5ACXX:8:2204:5918:177738/1 +CCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGN ++ +JJJJJJJIIJJJJIJIJJIIIIIJIJJJJJJJJJIJJIJHHHHHFFFFFFEEEEEEDDDDDDDDDDDDDDDDCCBDDDDBDDDDDD< +@HISEQ1:121:C0EP5ACXX:8:1103:3073:115589/1 +GCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTT ++ +GGAHHHEHHJIEDDFA@GGGB@?DBD?FGGC:BD<)8=8=C1(@@DG;DCHFHECE;CD@3;A;=>=CB@ +@HISEQ1:121:C0EP5ACXX:8:2202:7695:181317/1 +CTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATT ++ +IIJJIGIIIJJJGGGIGGIIIIJJJGJIGGBCHGGGGA3=C@HH@GHGFEHBC@=@BDC@CBADBDDCCDCCC@CD@CCDCDDCCDC 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+IJIFHHJGIJJEHGJJIJJDGGHJJJIJIIJIJICHHHIGJJII3=>AGHIGGG@GHHGGFDDDDECEECBDDCCBDCDCDDBDDDB +@HISEQ1:121:C0EP5ACXX:8:1205:6454:8959/1 +TCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGNN ++ +JJJJIJJJJJJJJDGIJJIJGIGIIIIJJIJJJHJJJJJJJJJJJJJHHHFFFFFFEEEEEEEDDDDDDEEEDCDACDDDEDDDDDD +@HISEQ1:121:C0EP5ACXX:8:2105:5499:95549/1 +AGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTT ++ +JIGBCHGA@GEH@FFHIBHEH@HEGICEECHFD>BCDDD>>?CCCDDC@CCCDCDDDDBDCCCCDDDDDDDCCDCCCCDDD>ACCCA +@HISEQ1:121:C0EP5ACXX:8:2303:18227:25094/1 +TGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTC ++ +JJJJJIJJJJJJIJJJIIIIIIIIJGIJJJJJHIJJJIIIHHJJJJJJIJJFIIIJHGGFFFFFEEEDECCBDDCDDDDDDBDDDCD +@HISEQ1:121:C0EP5ACXX:8:2305:9755:5948/1 +AGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTT ++ +JJJJJJJIIJJJIIIJJJIIJJJJFJGJHHGFDDDDDDDDDDDDDDDDDDDDEDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:1203:20148:178661/1 +AGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTN ++ +JJJJEGIJJJJJJJIIJIJGGHIIJIIEEHIIHGIDGAGGIICHDGIJIIGIJJIEFFHFBBCFBCCEC@BDDDC2@CCCABBBD9? +@HISEQ1:121:C0EP5ACXX:8:1306:5394:199706/1 +AAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTC ++ +JJJJJJIJJJJJJIIIGIJIJIJJJJJJIHHHHHFFDDCDDDDDDDDDDDDDDDDDEDDDDDDDDDEDDDDDDDDDCDDDDDCDDDA +@HISEQ1:121:C0EP5ACXX:8:1307:18623:18950/1 +AAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTC ++ +JJJJJJIJJJJGJJJJJJIIJJJJJJJJJHHHHHFDCDDDDDDDDDD@DCDDDDDDEDDD?BBDDDEDDDDDDDDDCDDDDDDDDEC +@HISEQ1:121:C0EP5ACXX:8:2206:14733:35674/1 +AAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTC ++ +JJJIJIJJJIJGGGJJJJJJJIJIJIJJJHHHFFFDCDDDDDDDDDDDDDCDDDDDEDDDDBDDCCEDDDCDDCCDDDDDACDDDDC +@HISEQ1:121:C0EP5ACXX:8:2204:18585:104307/1 +TTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTC ++ +IGIII9:BGHHBFHIGHGBGCBAEAFHIIIE@CFH@EEAE=?CE=B;?BCCCCCCBB?BB@ACBC@C +@HISEQ1:121:C0EP5ACXX:8:1207:19105:92282/1 +CGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACN ++ +IIJJJJJJJJJGIIJJIBEIIJGIIIJJIHHHHEEFFFDDDDDDDDDCDDDCCDDDCDDEDCBBDDDDADDDDDBCCCCCCDDDCDA +@HISEQ1:121:C0EP5ACXX:8:1301:17377:139560/1 +CTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATT ++ +E@EDCDIEFEEIDE9ECEIIID9D<6@DEE*=8==BC@C@@DDEEIACDCDC>DD>ADAAA@7>38?>AADA>DAAA>AAAAA:4>> +@HISEQ1:121:C0EP5ACXX:8:2203:19760:174167/1 +TTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAG ++ +EAFGIEGBC3C3EEHIIA4A5:5@@>A>?3>A>AA>44>> +@HISEQ1:121:C0EP5ACXX:8:1107:9791:182343/1 +GGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAG ++ +GI=FGHIIJJJIIJJIJIIGGHIJG?DHIJJJJJGIGGFGGGJIJHIJHHHHHHFFFECDDBCCDEDDCDDDCDDDC>ACCEADCA< +@HISEQ1:121:C0EP5ACXX:8:1104:5226:71069/1 +CGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTG ++ +DDF6E@FBF9EFIF@F@FFEBE1@67C7=ACEC?C@BDBB>@>>>A@:>:?BBA3:@3(4:<9BB2+>:+>A>@BB:A +@HISEQ1:121:C0EP5ACXX:8:2306:9426:60664/1 +GCGAAAACAGAGGCGAGGAACGAAACTCATTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGNNNNN ++ +EB68:CCC@CCCCAC:@>((4>>?@@@C@ACCC +@HISEQ1:121:C0EP5ACXX:8:1106:9391:87088/1 +AACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTC ++ +IJIIJJJIJJJJJJJJJJJJJIJGHIIJJJJIIIHJIGIJJJJJIIJJIJJJGHGIGIJHHHEEEDDEFEEDCEEDDCDDBDDCCCD +@HISEQ1:121:C0EP5ACXX:8:1202:13276:64787/1 +AGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTATTATTTGGAGTCTACTGCAGAAG ++ +@G;CCC9EBED:CG;F).BF)8=;8C))))=)=AACH3?CDEEB +@HISEQ1:121:C0EP5ACXX:8:2302:2707:156790/1 +GGTGCTTGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCN ++ +GIC=AFH@CFDDFADGA@DFBFCE@B>FEF<@FD@DFF4@@EE@@:=?=2=;;;)7.>A:6(.3(5=?@BAB>A4:>@> +@HISEQ1:121:C0EP5ACXX:8:2108:9892:29175/1 +CTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATAGAAGGCTGCTCTCACCGGAATCTCTTCACTTGC ++ +HIBHIIIII@@AF@?GAFEGCGGDAGGAFH*=B=FB>=>.=FDHG)7===EH=??C37((6;=3'3<>>@;(:>>@CCC +@HISEQ1:121:C0EP5ACXX:8:2206:3357:101994/1 +TTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGN ++ +JJJJJJJJJJJJJJJJGJJJIJJJJJJGIJJJJJJJJJJJJJJIJJIAHIIJIIJIGHHHGHFDFFFEFDEEE@@CDFEC?CB@A33@C@CCB@BB588339<8505<5A?B@B@;AACAC@::3:8359<55?C((+:?@9>:(:4@>:> +@HISEQ1:121:C0EP5ACXX:8:2303:12137:88145/1 +TTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTAAAGAGACTGTAT ++ +JJJFIJHHIJJJIIJGIIGHHIJGJIJIGIJFIIJIJFDHIIIJIIJJIIJIHHHHGHFFFDCCDEBDDDBDD@CCDDDDDCCD>CC +@HISEQ1:121:C0EP5ACXX:8:2107:6159:66543/1 +CCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCANNN ++ +JJJJJJJJJJJJJJJJC9BDBCDDEDDDDDDDDDDDDDDDDDDDDDDDDDDBDDDBDDDDDDCDDDDDDDDDDDDBDDDDDDDDDD: +@HISEQ1:121:C0EP5ACXX:8:2207:2890:5397/1 +AACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTG ++ +EHBFHH?C?C@CCCCB@<(>>@@CCDDD>9?>B +@HISEQ1:121:C0EP5ACXX:8:2304:18462:130846/1 +TCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTT ++ +@D<DF>BG>FF@@@)=/=;;))8)7@E@AACEFFDBBDDC@B@A>>@2=;8=A@BAAAAA@:A:@@: +@HISEQ1:121:C0EP5ACXX:8:1105:9051:178143/1 +AACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGGGC ++ +JJIIIJJGHIIIJI@EHICCHGIIJGIJIIIJJBGIEHJJCGIIJIJJIIJJJIIEHEHHGFAEHFFDBDEEDDCBCCA>CBCDD@< +@HISEQ1:121:C0EP5ACXX:8:2101:7366:6467/1 +TCTAACCTTGGGTTGTGGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCNN ++ +GGHIIJIIJJII?FF?DG?FDHIGIJJJGGGIG@AE@059;BBDDCCDBB55>B@<25>@<&4@CCDCCC +@HISEQ1:121:C0EP5ACXX:8:2201:18060:138565/1 +CGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGN ++ +JJIJJJJHHIJJFIIIGIJIIJJIIJIJIIJIIJJJJJJJJJIJIIJHHHEHHFFFFFFEEACEEDDCCACCCDECCDDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:1203:1544:189212/1 +CGAATTGAAGCCCTAACTCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTAAAGAGACTGTATTCTTCAGCAACAATCAGATCC ++ +JJIJJJGIIIJJJJHGIIIIJJJJJJJIJJGIGIJJJJJIIJJJJIHHFBDDDCDDDDCCCDD>CDEEEECDDCDDDDDCCC@CAC@ +@HISEQ1:121:C0EP5ACXX:8:2206:11441:98185/1 +GAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTG ++ +JFHIJJJJJHGIIIIJJJJIIHJJJJIHJGIGIJJIIJJJGHIJFHI@FHIJJFCEGEEHGDFFFFCECEEEEDDDCDDDDCDDDD +@HISEQ1:121:C0EP5ACXX:8:1302:13085:192464/1 +ATCAAACCGATCTAACCTTGGGTTGTGGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGNN ++ +JJJJJJJJJIEIJJJGIJIIJJDGIFGHBGHIIJJJGJJIJJHHHDD?CCDEDDC>:?CCDCBCGBBG9FAE7@@E@77ACHFDDCDFCEAAC@@ACCC<:AC +@HISEQ1:121:C0EP5ACXX:8:1108:18185:47615/1 +TCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGG ++ +C?8:?G?:D3&&003>3@>A@A38B<(>)5<5<>(9ABB +@HISEQ1:121:C0EP5ACXX:8:2105:7748:124139/1 +GATCAAATAAATCAAACCGATCTAACCTTGGGTTGTGGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGG ++ +IGEDEGGIIJJGHHJJJGEIJJGHGJIJEIIG?C<@F=FEGHIICEHHAF?DA>ABACCC>CCDDDDBDB->ACCD? +@HISEQ1:121:C0EP5ACXX:8:1201:13322:122364/1 +GACTGTGTAAGCAAAAGAGCATACAAACCTTGGGTTGTGGTTCCAGCAACGAAGGGGGGTTGTCAATAACTCCTTGCGAAAACAGAG ++ +9@FHCE>CHFDHDGIEEEF9EGIGHG@?DEEGIIHEGGHIHCFHIGGHEGHHD=BDCBB5559>(:>AA4:>C>@:@<-59@38CCA +@HISEQ1:121:C0EP5ACXX:8:2107:6281:156438/1 +GGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCNN ++ +EBBFGCHFHIIGHHHEFAEGGHFGCGDFAD@>@C;>AAC@A +@HISEQ1:121:C0EP5ACXX:8:1305:12682:160339/1 +ATTGAAACAAGAGCCACACCAGGAAAGAGCCTTGATCAAATAAATCAAACCGATCTAACCTTGGGTTGTGGTTCCAGCAACGAAGGG ++ +HIIJIJGIIJIIJJJJJFEHJIIHJJ@GD@GIJIJJJIIJJJIIGHIJIJJJHHFFFFEDCCCCBBDBBDDDDDDDCCDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:2101:10614:180991/1 +TCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCAGATC ++ +GIEHHIJFGI@HGFHIJJIJDBE@DEEEECACDDD?BBBBCCCDDDD3? +@HISEQ1:121:C0EP5ACXX:8:1105:5527:6171/1 +AACTATAGAATTGAAACAAGAGCCACACCAGGAAAGAGCCTTGATCAAATAAATCAAACCGATCTAACCTTGGGTTGTGGTTCCAGC ++ +JJJJIJJJJJJJGHJIJJIJJJJJJJJJJJJJIIJJJJGIJJJGIIJJJJGGIJJJIHHHGDDDED@CDDDDDDBDDDDBC@ACDD> +@HISEQ1:121:C0EP5ACXX:8:1207:4910:149486/1 +TCGGCGACCTAAAGAGACTGTATTCTTCAGCAACAATCAGATCCCCAGATTGATTTGCTCTGATGGCCGCTCTTGAAGGAGTTTCGT ++ +IIIIIIJHIIGIJJBDEFGIBBGHIIJJJEHJJJJIGEHCEEHHFB>?ACECCDCCCDDDCCCDDDDD@DBBBCDCCCCBB3>A@BB +@HISEQ1:121:C0EP5ACXX:8:2302:17741:148058/1 +CCAGATTGATTTGCTCTGATGGCCGCTCTTGAAGGAGGTTCGTTCCTCGCCTCTGTTTTCGCAAGGAGTTATGGACAACCCCCCTTC ++ +EG@G?AA?5?>?=/88?@@>@A?<<@><9@CAA98<95< +@HISEQ1:121:C0EP5ACXX:8:1305:1936:75650/1 +GTAAACAAACTATAGAATTGAAACAAGAGCCACACCAGGAAAGAGCCTTGATCAAATAAATCAAACCGATCTAACCTTGGGTTGTG ++ +CCAFHII4@>EAAEHCE>AHEDEB>?BB;;>CBCCC3??@@CC +@HISEQ1:121:C0EP5ACXX:8:1302:17121:81693/1 +ATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTATAGAATTGAAACAAGAGCCACACCAGGAAAGAGCCTTGATCAAATANNN ++ +GGGHGGIIJJIJJI@GGHGIGIGIIJE?DHIIHIIJEHGIJJJIJJJIJJJJJJJIJIGIEAEDFFFEEEEDDDDDDDDEDCADDDC +@HISEQ1:121:C0EP5ACXX:8:2205:3938:177351/1 +ACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGGGCTCC ++ +IGIIIIIIIGIJIJJJJJIEIJJJEGDHGHHHCHIJIIIJJJJJIHIJJGIDHIJJIFH@HHEFDDAC(6=CBCDDDCBCC?BB?B< +@HISEQ1:121:C0EP5ACXX:8:1101:11189:44094/1 +TGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCC ++ +JJJJJJJIIJJGHGIIGFIEHIJJJJJJJJJIJJIJJFEHIJJJIHHHHHFFFFFFFEDEEDDCCDDDDBDBDDDDDEDCDDDDDDA +@HISEQ1:121:C0EP5ACXX:8:1102:2324:141339/1 +GTTCCTCGCCTCTGTTTTCGCAAGGAGTTATGGACAACCCCCCTTCGTTGCTGGAACCACAACCCAAGGTTAGATCGGTTTGATTT ++ +JJJJJIJJJJIJIJGIJIHGIJJJJIIFHIDIJIIJJJGIIHFDCED?CDDDDDDDDDDDDBDDDDDDD@ADDDDDDDBD>B@CDE +@HISEQ1:121:C0EP5ACXX:8:2102:5334:25020/1 +ATAGTTTGTTTACTATTTTCTATAACCCTATGCCTGCATCAATTGGATCTGATAACCTTAACACCTATTGTCGCTCATGGTTTGAGN ++ +IJJJJIIJHHHJJJJJJIIIEFHHIIIIJJIIJJJIJIJJJIGHJJIJJIJJIJIIJJJIIIJGGGEHHHAHFFFFDCCECCDDCD9 +@HISEQ1:121:C0EP5ACXX:8:1208:3562:49824/1 +CTTGAAGGAGTTTCGTTCCTCGCCTCTGTTTTCGCAAGGAGTTATGGACAACCCCCCTTCGTTGCTGGAACCACAACCCAAGGTT ++ +IJJJIJJIIJIEHIGIFIJIJIIJIIJJHAHEGGGIJJFHGHDEFFFFDCDDBDDDDDDDBCGBCFEDFB@;EEAEE?BDD@<@B@(;;>@@?88:2:????B8(8>?<8?:@A8 +@HISEQ1:121:C0EP5ACXX:8:2303:6312:178128/1 +ATATTTCCGGATCCAATCAATCTCAAACCATGAGCGACAATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGCATAGGGTTAT ++ +JJJJJJJJJJJJJJJJJJJIJJJJJJJJJIJJJJJJJJIHHHHH?CDFFFEEEDEEDEEDDCDD@CAACCCC@C<<8@>CD?CBB: +@HISEQ1:121:C0EP5ACXX:8:1202:14487:9079/1 +ACGCAACACCATATTTCCGGATCCAATCAATCTCAAACCATGAGCGACAATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGCN ++ +FFB8F8FF@C??BF?:??B6)0??DDBBDFF<=CB)8=@=D4CAEF><>/6@A>-5;;55;>5>>AB@;@@AB>:@:(>>BA:A?>8 +@HISEQ1:121:C0EP5ACXX:8:2306:19017:130779/1 +ACTCGGTAAGACTGAACGCAACACCATATTTCCGGATCCAATCAATCTCAAACCATGAGCGACAATAGGTGTTAAGGTTATCAGATC ++ +IJJJJJGFHIJIIJIJGGEHIJJGIJGIJJJJHIJJIJIIIJJJJJJHEHHHHFFFFFEEDDDDDDCCD>A5?CDCDCCCC@CDDCD +@HISEQ1:121:C0EP5ACXX:8:2204:5708:174080/1 +CTCTGTTTTCGCAAGGAGTTATGGACAACCCCCCTTCGTTGCTGGAACCACAACCCAAGGTTAGATCGGTTTGATTTATTTGAT ++ +HGIIJJIJJGIJIJJJDH@FCGHIJJJJGIJJJHHHHFEFFCCCCACCBBDDBDDDD4@ +@HISEQ1:121:C0EP5ACXX:8:2107:10276:107947/1 +GATCCCCAGATTGATTTGCTCTGATGGCCGCTCTTGAAGGAGTTTCGTTCCTCGCCTCTGTTTTCGCAAGGAGTTATGGACAACCCC ++ +3F?DGHHE@DBGGGG@B;=8;CG@EGE>EE8B8ACCCC@>?CBBB==8?B3(>CCA>+><@<<> +@HISEQ1:121:C0EP5ACXX:8:2201:2168:144674/1 +TACAACGAAAACAAGGAATGAGATTACTTATAATATACTCGGTAAGACTGAACGCAACACCATATTTCCGGATCCAATCAATCTCNN ++ +JIIIJIGIJJEEGGGJIIJIJGIJIJJGGGGGIJJIJJIIIIIHHEFGIAHGHIBEFFEDD?CEDEDCCDD@DDDDCDCDDCDDCDD +@HISEQ1:121:C0EP5ACXX:8:2301:14772:138623/1 +CTTACAACGAAAACAAGGAATGAGATTACTTATAATATACTCGGTAAGACTGAACGCAACACCATATTTCCGGATCCAATCAATCTC ++ +JJJJJJJJJJJJJJJJJJIJIJJJJJJIJIJJJJJJJJJJJJJJFHJJJJJIJJJHHHFFECDDDDDEFEEDDDDDDDDDDDDDDDC +@HISEQ1:121:C0EP5ACXX:8:2306:2564:73699/1 +CCCTTCGTTGCTGGAACCACAACCCAAGGATAGATCGGTTTGATTTATTTGATCAAGGCTCTTTCCTGGTGTGGCTCTTGGTTCNNN ++ +EGGIGGI3?CBDGCDBFH8)??@DHIII?(=CC@@A=AEBCCCC(:?3:@C(5:?5922?88>CC@(48>>CC +@HISEQ1:121:C0EP5ACXX:8:1303:13585:40340/1 +TGCGTTCAGTCTTACCGAGTATATTATAAGTAATCTCATTCCTTGTTTTCGTTGTAAGATTAGTTATGTTTCCCTGGCTTATTCTNN ++ +HJJJJJJIJIGIIIJIJBG?FHIIJJJIIJEGHIJIJIJJIEFGGFHIJJJEHIGEEEHHHFFFFFFFEEEEEEDCBBDDDDEEEE@ +@HISEQ1:121:C0EP5ACXX:8:2107:18091:187815/1 +TTCTAACTAGATTAGAATAAGCCAGGGAAACATAACTAATCTTACAACGAAAACAAGGAATGAGATTACTTATAATATACTCGGTNN ++ +EGHGHIGGGCDHHGIIIGGCFGHJIJJHGIEHJIHIIEHJIGGHIGIIIEIIIJIEEHFFFCDECCEEEECEDDEEEEECEDDB8A@ +@HISEQ1:121:C0EP5ACXX:8:1206:20456:140956/1 +TAACACCTATTGTCGCTCATGGTTTGAGATTGATTGGATCCGGAAATATGGTGTTGCGTTCAGTCTTACCGAGTATATTATAAGTNN ++ +JIJIGGIJIJIIIGJGAEGEGGFEGIFACHGIJIIIIFHFHGG7@FHGGEH@A=CEEFECCCA;A>CDD?B/=8 +@HISEQ1:121:C0EP5ACXX:8:1305:4292:178325/1 +TCGCTCATGGTTTGAGATTGATTGGATCCGGAAATATGGTGTTGCGTTCAGTCTTACCGAGTATATTATAAGTAATCTCATTCCTT ++ +HIIIJIJIGGEHEGGGIIIEECEGGHEEHHFAFGGHGBCB=FCGHIHEAAEDDE>@?A>>@ACCAD@CCCC +@HISEQ1:121:C0EP5ACXX:8:2201:1091:169035/1 +GGTAGAGGAATCTATCTAACACACTCTCCTGCAGAGCAGCAACAAAATTGATTCCAATAATACATCTAATCTTGAGATCCAACATGC ++ +HGEHG?CCEEEEECC@@CBCCCC@C?CCC +@HISEQ1:121:C0EP5ACXX:8:2201:15300:19470/1 +TTGTCGCTCATGGTTTGAGATTGATTGGATCCGGAAATATGGTGTTGCGTTCAGTCTTACCGAGTATATTATAAGTAATCTCATTCC ++ +JIJJIIGHJGHIIFGGIBHAEGIHIGIJGGGIIJ@FIJJIIJ@FCCHIHEEDFFFFFEEECBBD=ACDEDDDEEDCDDDDCDCDDE@ +@HISEQ1:121:C0EP5ACXX:8:1308:14340:140874/1 +GTTTCCCTGGCTTATTCTAATCTAGTTAGAATTGATCCTTTCCAGTTGAGACTGAGCATGTTGGATCTCAAGATTAGATGTATTA ++ +F:@;@ +@HISEQ1:121:C0EP5ACXX:8:2202:12780:47547/1 +ACAACCCCCCTTCGTTGCTGGAACCACAACCCAAGGTTAGATCGGTTTGATTTATTTGATCAAGGCTCTTTCCTGGTGTGGCTCTT ++ +CIIGIHGGIIJGIDDGBBFGGGIIGEIEGGGHEIII;=AHAHBDFACDD;>@3>CCD@@CC>A335:?ACCCC@:?4<(2<8?>CC +@HISEQ1:121:C0EP5ACXX:8:2106:13356:92925/1 +ACAGAATAATCACAAGGCTTGAGCAAAGGTAGAGGAATCTATCTAACACACTCTCCTGCAGAGCAGCAACAAAATTGATTCCNNNNN ++ +JIEEIHBGGGIIIIIGHJJIHJGIIJJIC:BDFACHHIHJGGHIIJIJJJIJJJJJJJJHHEHFDFEFEEEBDACD>ADDDFFACCA +@HISEQ1:121:C0EP5ACXX:8:2206:14713:40562/1 +AGAATAATCACAAGGCTTGAGCAAAGGTAGAGGAATCTATCTAACACACTCTCCTGCAGAGCAGCAACAAAATTGATTCCNNNNNNN ++ +IIIEGGIIGIGGIECIIIIIIIIIIGIBB@D9BFCEFHIIIIDFFHGGICCGHGCDHGGCEAEFFD@AC2>ACDDDDDA@5:AAC:> diff -r 000000000000 -r 05c27700e5ca demo_files/mother_2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/demo_files/mother_2.fastq Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,704 @@ +@HISEQ1:121:C0EP5ACXX:8:2204:19496:144054/2 +AGGGGCCTTAGCTGGTGATCCGGGCTGTTTCCCTCTCTCCTCTAAAACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTC ++ +GIEIJIJGGHGAGHGFGGIGCHGEIJJAFDAEHIJGDHHGFHHHHFFDB?BCBDCCDDD>CCDDECDDDCEEDDD>CCDDCDCDDD@ +@HISEQ1:121:C0EP5ACXX:8:2204:8525:81513/2 +TCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCC ++ +JJJJJJJJJJJJJJHJIJIJJJJIIIIIJJJJJJJJHIIIJJIJIJJJFFHGIJJJJJGGEHHHFFFFFEDDCEDDDDDCCCCCDDB +@HISEQ1:121:C0EP5ACXX:8:1103:3495:189629/2 +TTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCCCCACAATTTGCAAGGGCAAATTATGTGTTCCACCACAAAATGAAACAAGAA ++ +FEGHGIIICDGIJHHGIIGJFHIIJIHIJIIIGF=DD?C>ABCDDDDEDD?B@BBBDDDEDEEDDDDEDDDDDBDDDCDCCDCDDDD +@HISEQ1:121:C0EP5ACXX:8:1304:11225:78484/2 +AAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCCCCACAATTTGCAAGGGCAAATTATGTGTTCCACCACAAAATGAAAC ++ +HCEBH@HGIIIB?+=>A;3,;?CA5:>;>>@@B@D<::44>++43(:>:?ABA?CCDCDDD?BBB@BDCCAC@DDDDCACDDDDDBD@@CC> +@HISEQ1:121:C0EP5ACXX:8:2205:18768:173013/2 +TAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCCCCACAATTTGCAAGGGCAAATTATGTGTTCCACCACAAAATGAAA ++ +EHGHIHJGIJJIEIEFICGIHIIJDFGGEHCGGGIJ?DGGICCEFFFBBDD@@CCDD@?BDCCCCD3@@??@@D +@HISEQ1:121:C0EP5ACXX:8:1206:13113:50926/2 +GAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATT ++ +7<:23AGE9*?@BFDABDFBFFB;E=FCHFEBGIIFH@@CGGHCEEHHBHDF?;@:@A@;@ +@HISEQ1:121:C0EP5ACXX:8:2305:13995:134971/2 +AAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCCCCACAATTTGCAAGN ++ +EHGGGHIJJGGBGHIIIJHGIIJBBD?FG9DGIGDFFFHIJJJIHIEGGGHIGHGEADFF>DCDDBBB9@?AA@AHEEEHDD3?CDABBDDDD3(4@CC2 +@HISEQ1:121:C0EP5ACXX:8:1302:11743:35278/2 +GCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCCCCACA ++ +AE@@GGGBDADHIGHCCBCCFDB*9?BC?F9*?DBGBFFBC=@DHIEEHA@EDE.7@DE;@;@ACD@ACDDB<8=?>9<&<::??9? +@HISEQ1:121:C0EP5ACXX:8:1307:11530:167684/2 +GCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCCCCACA ++ +EHJBHIFGHIGEGIIIGGGDDHHEHIIG?FABF?@FBFCCFEGG=@CDGCHCCH??>>;;?>CE?D=@CCBBDDB69@D><>48?5< +@HISEQ1:121:C0EP5ACXX:8:2306:2962:37980/2 +TCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTAT ++ +GHGBHEBAHEEHGGGIJJJECFDFBDADGHEIIIGIIHIGD@F;BFCFECHIICGGCE).=CCECDDF).7(3;,955? +@HISEQ1:121:C0EP5ACXX:8:2307:9346:102436/2 +TTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAACC ++ +IIIIIHGJJIGJEHICFED@2C*:C*1C*:8B9BD49?**?B*8B +@HISEQ1:121:C0EP5ACXX:8:1202:8720:147817/2 +TCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCC ++ +JJIJJJIIJIIIGIJIGIIIJGIJJIJJJJJJJJJJIJJJJIJJIIJGI@FGHIIGHGEEEHFHFFFFFDEDCEDBDDDDDDDDDDB +@HISEQ1:121:C0EP5ACXX:8:1203:20081:59684/2 +CCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAAT ++ +JJJJJJGJJJJJJJJIJIJJJJIJIJJJJJJIJIJGFHII@GIIJJ?CHHF@CBDFFEEED;ACDD@CDDDDD8>CDEBDDDDDDDB +@HISEQ1:121:C0EP5ACXX:8:2202:6060:140689/2 +CCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAAT ++ +JJJJJJIJJJJJJJJJJJJJJIJIJJJJJJJJJJJIGHIJDHIJJHAEHFFBDEFDEEEED>CDDD@CDDDDD?@CDEDDDDDDDD> +@HISEQ1:121:C0EP5ACXX:8:2206:18846:173028/2 +CTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTC ++ +IHHGIGIEHCH9FACDDDDCCDDDBDD +@HISEQ1:121:C0EP5ACXX:8:1205:18182:73982/2 +GGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAA ++ +JJJJJJIIJJJJJJJJJJJJJJIIIIHIJJJJHIJJJIJJJJJJJJJJIIJJJJJJJJIHGDHFFFFEEEDEDDDEEDDDDDDDDDC +@HISEQ1:121:C0EP5ACXX:8:1206:1811:22216/2 +CGATCTGAGAACCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGG ++ +H@CCEEHIIEGGGHCGHDHIIGAHIEIEGEE@AF=E@;;6?E;?BD?DF;A;;>A@BA9=>C(;;BACCCD?>@A@4(:4>?>B +@HISEQ1:121:C0EP5ACXX:8:2307:19323:17727/2 +CAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTNNN ++ +IHIJIJJJGGIGIJJJJJJIIJJJIJJIJJJJIIIHHHFEFFDEEDBDDDCDDDDDDDDDDEEDCEEED:ADDDD8?BCC@A>CBD: +@HISEQ1:121:C0EP5ACXX:8:2304:13953:99797/2 +GAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTN ++ +JBC;HFGEIIJIDGIGHHIG=D@EAAGHGIGEGHHF@BFFEDDDDDCDBCBDCDDDDDDDBDDCCCD@CACCDDDDDCCD +@HISEQ1:121:C0EP5ACXX:8:1206:2780:83786/2 +CGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAA ++ +FA@FHB6;F6HCHICCA@FGEEHGIEG:C@5@.BE>?AEBAAECD@CCDBDDDBDDB?CCCBDDBDCDDCDCBBDD?CCCDEDCDD> +@HISEQ1:121:C0EP5ACXX:8:1302:14767:71234/2 +CGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAA ++ +JIJJIJIIJIGIJJJJJIJJJJJJJIIGIJJJJIIJHHHFDDEDDDDDDDDDDDDDDDDDDDDDDDDDDDDC@DDDDDCDEDD@CC> +@HISEQ1:121:C0EP5ACXX:8:2103:4557:157261/2 +CGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAA ++ +GGB1?DDGIHCHIIGHDGGGDHIEGIIGEFHGICHEHFEFDBEE@@CCCB??BD??B?>@: +@HISEQ1:121:C0EP5ACXX:8:2302:4919:198649/2 +TCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAA ++ +JJJIJJIIIJIJJJJJIJJJJJJJGJJJGHIJIIJIIHHHFDDEDDDDDDDDDBDDDDBCCCDDDDDDDDDDDDDDD?CCCDEDCDD +@HISEQ1:121:C0EP5ACXX:8:2102:15481:17585/2 +TTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTCGGTTCC ++ +GIJIJGIJIJJFGJIIFHHIIJJJIJIIJJI@GHIJIIJIIIJJJJIJIIIJJJIIGHIFHFED@CDFFDEEECB;?@DDDDDBDBA +@HISEQ1:121:C0EP5ACXX:8:1102:3776:50474/2 +CTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGT ++ +JJJJJJJJJJJJJJIJJIIJJJJJJ@GFHIJJIIJJIIIJJJJJJIICGGHJGHIIJIJJHIGHFEEFFFFFEEDDCDC@>CCCCCB +@HISEQ1:121:C0EP5ACXX:8:1106:16133:150529/2 +TCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTAT ++ +IGIJAEBEDCBCCBDDDDDDEEDCACC +@HISEQ1:121:C0EP5ACXX:8:1103:1745:180624/2 +CAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAANNNNN ++ +JJJJIJJIJJJJJIIGJJJJIIJJDIJIJJJJJJJIIFHIJJJIJHHHEBCDDEDDBBDDDD=BDDDDDCDDDBDDDDDDCDDDDC@ +@HISEQ1:121:C0EP5ACXX:8:1206:17568:25304/2 +CAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAANNNNN ++ +IGJGIJEGIIIJJJIJIJGIJIJIIIHGHJJIFDGGGHGDGGGIEEHHFDEC?@BBB?CDD@DDDDCDDCDACBBDB@BBDACBBC? +@HISEQ1:121:C0EP5ACXX:8:2105:5209:169114/2 +ATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAANNNNNNNNNNN ++ +GIGIIIEHIIGHDBEHGIGJBHIIFGJJJIGJJJJJIIJGIGHHADEEFCDEEDBDDDDDCDCDDDDDDDDDD???CBBDDCCEDBABDB??BCCCDCCBDDDDDDDDCCCDDDDDBDDDDCCBDD< +@HISEQ1:121:C0EP5ACXX:8:2306:11471:141288/2 +TTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACACTTAACCCTT ++ +HGJBEHIGHGGH>CGIGGJCIIIGHIIJIJJJFIIIIGEEIIJJGHJJJHFCCACDCDDDDCCDBDC +@HISEQ1:121:C0EP5ACXX:8:2107:3840:161938/2 +GGATGCAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAA ++ +@+2++++2+2:?*1:B;:35:A<<:>A +@HISEQ1:121:C0EP5ACXX:8:2302:17167:90156/2 +AAGAGATTCCGGTGAGAGCAGCCTTCAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCNN ++ +IJJJJJJJIJIJCGIIJJJIIJJIJJJJJJJIJJJIIIIJJJJJIJJJJJJHHFDFDDDEDDDDDDDDDDDDDD9ADDDBDBDCDDD +@HISEQ1:121:C0EP5ACXX:8:1305:4289:116518/2 +ACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGT ++ +JJJJJIJJIJJIIJJJJJJIJHIJIJJIIJGIJJJJIIIHHGIJJJJJJJJJJJJJIIHHHHHFFFF>CCDEEEDDDDD@BBDDDBD +@HISEQ1:121:C0EP5ACXX:8:1201:10878:193365/2 +ACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCT ++ +JEHIGGIGHIJIIIIJJIJICHGHHIGGHGGJGCHEHHGGH@FHHEGIHIJIHHICDHGEFEF@;?=?@C>A3;@?5;;=>@CDD +@HISEQ1:121:C0EP5ACXX:8:1107:3570:34778/2 +ACACACTTTTTCCAACTTCATTTATGAGATTGTTCAACAACACGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGGGCTCCTCTNNNN ++ +IJJJDIJJJJGGIIIJIJJJJJJGIIJJIIHHIGCIDFGHHGIIGJJJGIIIEHGIGIFHHFFF@DEEEEEDDCDDDCBBDDDDCDD +@HISEQ1:121:C0EP5ACXX:8:1104:15089:78984/2 +TGTGGGCATTCGCCCCGTATACCCAAAAATTTACCCATCAACACTTAACCCTTACTTTACAATTGCCTCTCTTTCGATTTTTGCTCC ++ +JI +@HISEQ1:121:C0EP5ACXX:8:1101:10457:23604/2 +AGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTTCAATCAATCTCCAATCACCATTCGCAGGNNNNNNNNNNN ++ +JJJJJJJJJJJJJJJJJJJJJHIIJJIJGIJIIJJHFHIJIJJJJIJJJJJJJHHHHHHFFFFFFEEDEEEEDDDDDBBDDDCDDD@ +@HISEQ1:121:C0EP5ACXX:8:2305:17031:5327/2 +ACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTTCAATCAATCTCCAATCACCATTCGCAGGNNNNNNNNNNNNN ++ +CGGGAGEE:HC:FHFHHGI:4?FH@CEF@?A9A).7@DEEE<'399=@@DD?@CC@@>:>?@ +@HISEQ1:121:C0EP5ACXX:8:2102:10309:35842/2 +AGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTT ++ +JIJJJJFHIHIHJIIJJJJJIJIJJJJJJJIIJJJJIHHHHHHHFFFFFEEEDEEDDDDDADDEDDD?CCCFDD>B@DACDDDBDD> +@HISEQ1:121:C0EP5ACXX:8:2203:18766:43466/2 +AGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTT ++ +IIJJJJDGIFGEIIJJJIJJIJIIJGIIJIJJJJIJIIFHHHHHFFFFFFDEDEEDDDDD@CDEDDD@DDD;CB5<@BCDBDDBDDC +@HISEQ1:121:C0EP5ACXX:8:1308:4675:83154/2 +GATAGGGGGTTTAGTTAGGGCTTCAATTCGTGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGTTGAGAGCAN ++ +AFEACGEGG?D)*0**00?8?DB)/*B@8B)-5;@9C>>@D@CEH3=;A3@>C??C@@?C?A@-;>@A(:(,+8ABC?:9 +@HISEQ1:121:C0EP5ACXX:8:1107:5242:86751/2 +GAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCA ++ +JGIDHIIJJJJDGGGIIIGIJIFIIICHIJIJJIGHHHHHFFFFFFEEEEEEDDDDDDDCBDDDD:CCDDC<@<: +@HISEQ1:121:C0EP5ACXX:8:1306:15890:88846/2 +GAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCA ++ +JGHEHEHIJJJDFHHIGIGGIICHHGGEHIGGHGGHHHHHFFF?DFEEEEEEACCDDDDCBBDDDCDDDDDDDDDCDCD>@BDDDD@ +@HISEQ1:121:C0EP5ACXX:8:2103:4321:176641/2 +TTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTATACCCAAA ++ +IJIFHIIGGJJIIJJJGIIJHGIGIIIJJIIICFGGGHHIIGIHJJIIGIIGHIJJJIIHHHCE=BCCDDA=BDDDD<@DDDCDCDB +@HISEQ1:121:C0EP5ACXX:8:1104:18369:49451/2 +TCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGANN ++ +JJIIFHGHGHIJJJ?FHFIGHIJEIJIIHGHHGHFFFFDEEDEDDDCDDCDDDDDDDDDCDDCDBDBDACDEDDDDDCDCA<0<CDDDDDD@CCDDDDDDDBDBB:>ACDDDDDDCA +@HISEQ1:121:C0EP5ACXX:8:1202:4892:45787/2 +TGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCC ++ +JGHIJJIIHGEF>>CGHHIIJGEGIGGGICDDHEGHEHCHGIIGIEEHFHFCDBCFFECACDDDCCADDDBDBBC>CDC4:4>C>@? +@HISEQ1:121:C0EP5ACXX:8:1303:12868:89901/2 +GCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTC ++ +IJJIIEGIIIIIIIGIEGGHJI@AE@EDEFFBBCECEEDDEDBDD@DDDDDDDD>CDACCCDCDDDDCDDDDD?CCDDDCDDCA@CCDCDDDD?B@CCDDCDDAAC +@HISEQ1:121:C0EP5ACXX:8:2303:17380:176758/2 +GCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAANN ++ +GHJJJJJJJJJJGHIJJGHBHGGIJJJ':BBD;BEDEEDBDDDDEEDDEDDDDDDDDDDACDDDDDDCDDDDDDDCDBDDB@CDED: +@HISEQ1:121:C0EP5ACXX:8:1301:11188:179944/2 +ACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGGGCTCCTCTGCTCCCTN ++ +JJJJJIJJIJJJJJJJIJJJJJJJJJIJFIJJJJJIJJIJJGHIJJJJIJJIIIIIGGHHEDFDFFEDDEEDDCDDDDDDDDDDDD: +@HISEQ1:121:C0EP5ACXX:8:2306:14700:199855/2 +AAACTTTACCCATTAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTN ++ +IFEGDHGGEHIIGI@GIIICGIHGGGBFGGIDIEHAFGIEGDHIIGIIIIIIGIHIJGHHGFFFFFECD;>CCDEDCCCBB@BD@C@ +@HISEQ1:121:C0EP5ACXX:8:1105:6834:23521/2 +TCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGN ++ +JGJJJJJIFHFIIJGIIEIJJJIIIGIFHGHIJJIJHAABCDCCDDDDDDDDDDEEDDDCDDDDDCDCDCDDCDDDCC>CCCDCCD? +@HISEQ1:121:C0EP5ACXX:8:1304:15370:31007/2 +TCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTT ++ +GGGIJGHHCGGBHGHEGICCDGEGHHGGIGHEHGGIHHIIDHGHGFFGGFHFFFFFECDCCCDCDB=;?@CC@CDCACCDDDDDD>@ +@HISEQ1:121:C0EP5ACXX:8:1302:2247:98264/2 +GGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAA ++ +JJJJJJGIJJJJIJJJJJIJJJJJGGGGHGIJGGIJJJJJIIJJJJIJJJJJJIJJJJGHHGHFFFFEEEDEDCDEECDDDDDDDCC +@HISEQ1:121:C0EP5ACXX:8:2306:3485:63749/2 +AATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCA ++ +IJIJJJJIJJJJJJJJJHIJJJJFJGIIIJIIGHIJJJIJJJHHHFBDDCDCDDDDDDDDDDDEEDDEDDDDDDCDDDCDDDDDDCC +@HISEQ1:121:C0EP5ACXX:8:2208:8405:84311/2 +AGAATACAGTCTCTTTAGGTCGCCGAGAATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTC ++ +FBBF>IG>>ACDAHGIEHI+?DDCA@@(0*=;A@FBFH@@7@=CEHGDDBDDC@CDADDDB?A>C:>:?4:>@CCC +@HISEQ1:121:C0EP5ACXX:8:2302:12851:12461/2 +CGTATACCCAAAACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCANN ++ +IIGHHGHGIIIJEHIJJJGIIIC@GIHCGIGIIJIJHGGIJHHGHHHHFFFFCFFEEEEEDDDD=CDDDDBDDDDBDDB>CCDDDC: +@HISEQ1:121:C0EP5ACXX:8:1305:5063:120920/2 +TGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTA ++ +@>F@3ACEAHGDDAAEEDHCCDDDC@3?@?3BCDCDCCCBCDDC@ADDC?DC +@HISEQ1:121:C0EP5ACXX:8:1307:16680:41377/2 +GGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCN ++ +IJIJIJIHIIGIJJJJJIIIJJJJJJJGGGIIIJJJGBGGGIJGBHHHHFFEDDEEDDDDDDD@BD9@BDDCDDDDDDDDDACDEDD +@HISEQ1:121:C0EP5ACXX:8:1301:3542:41315/2 +TCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGC ++ +JJJJJJJJJJJJJJJJIJJJJJIJJIJJIJJJJJGJIIJJJJJIJJHIIIJIHFFDEEDDBDDDDCDCCDDDDDB5<>CC@ADDDD? +@HISEQ1:121:C0EP5ACXX:8:2202:5040:37535/2 +ATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGN ++ +JJJJIJJJGJJJJIIIJGIIGHIJJIIIIIIJIJJJHDGIIIJJGHIHGIJJJHFFDDEDD@?BDDAA::@CDDDD9>BCDCACC?< +@HISEQ1:121:C0EP5ACXX:8:1301:20965:126815/2 +AATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGN ++ +IJJJJIJIJJIJJIJJJJEIIJIIIJJIEIJJJJFIEHGGHIJEEGGIGHHJIHFFDDDCBDBD?ADCC@CDCDD>B9>@>CCCC:< +@HISEQ1:121:C0EP5ACXX:8:2208:7542:56931/2 +AAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAN ++ +CF94AHHIG9<@EGEGAGG?DFGIJD>F@9BF8DHHIGJJCGIIJJIIGD@@EHE>?BBCCBB?(;ACAC4@CAC@BD99>>CCDDC +@HISEQ1:121:C0EP5ACXX:8:1108:16683:76874/2 +GCAAATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCNNN ++ +JJJJJJJJDHIJJJJJJJIIJJJFHIJJJJJJJJJJIIJJJJJHHHHHFFFFFEEEDEDDDDDEDDDDDDDEEDDDDDDDDDDDDDE +@HISEQ1:121:C0EP5ACXX:8:2305:1262:195723/2 +TCCCTGCGNATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAA ++ +JJJJJJJJ#4AGHCHGIIJJIJGGIIIJJJJIJJJJIIJJIIJJJJIHHHHFFFFFDFEEEEEEDDDCDEEEDCC:ACDDECCDD:9 +@HISEQ1:121:C0EP5ACXX:8:2201:12777:169199/2 +ATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGT ++ +JIJJJIIGIEHIGJIJJJIJIJ=FHII?FGIJIJJJHIIIHGHJJIGEHFFHHFBEFDFDDD@BDDBCCBDBBBDD>C>CDDDDDD9 +@HISEQ1:121:C0EP5ACXX:8:1302:11283:198671/2 +GCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGANNNN ++ +JIJJJJJGIJJIJIJIIIJJJJJJJIJJJGIJJJJJIIJJJJJHIJHHHHHHFEFFFFEEEEECEDDDDDDBDDDDDBBBDD>C>C: +@HISEQ1:121:C0EP5ACXX:8:1206:5220:148135/2 +GAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAN ++ +IJIJIIHIJJJJJGIJGIIJGIIFIIJJJJIJCFHJHHJJIJIGGHHHGFDFFEEBDECEDDDDC>@BDD@D@DDDDAC +@HISEQ1:121:C0EP5ACXX:8:1105:12113:104911/2 +GCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGANNNNNNN ++ +IDHIJGJJHIHCGIIJJIGIGCEGEB6BGIIIJGBFGIJJJJIIGCHHGGCHFFFFFFFE>AABDBDDDDDDDBBB@>CA +@HISEQ1:121:C0EP5ACXX:8:2106:16519:145675/2 +GCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGANNNNNNN ++ +JJIJIJJJEHIIIJJJJJIJJJJJJIJJJIIJJJIIGHJIIJJJJJHHGHHHFFFFFFFEAEDDDDBBDBDDDDBDDDDDDCDDDDD +@HISEQ1:121:C0EP5ACXX:8:1201:11309:101312/2 +CATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCT ++ +GIJIIJJJJJJJJJJJIIJJJJJJJFHIDIGGJJJJGIJJJJJJIJJJIIHGIJJJJJH?CHHHFFFFFDDBDDDCC?>ADDDDDD< +@HISEQ1:121:C0EP5ACXX:8:1302:5526:110720/2 +TCCTATCTCTACAGTTTCCTATCTCTTCTTCTCT ++ +@3;A+,*0:0?D +@HISEQ1:121:C0EP5ACXX:8:2204:5918:177738/2 +GGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGATGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAN ++ +JJJJJJIIJJJJJJJJJFJJJIJJJ?FEIIGJEGGICGGJJJIJJIJIJHHFCHFFFBCDDDDDDEDDDDCDCDDDCDDDDCDCCA9 +@HISEQ1:121:C0EP5ACXX:8:1103:3073:115589/2 +GGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCG ++ +GGB@BBD9BDDDDDB?@B: +@HISEQ1:121:C0EP5ACXX:8:1301:8384:179301/2 +CCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGNNNNNNN ++ +JJIJJJJIJIJGIJJJJIJJIJIJJJJIJ>FIJIJJEIIHHHHHFFFFFFEEEEDCDDDDDDFDCDDDDDDDDCBDBDBDBDC>>B< +@HISEQ1:121:C0EP5ACXX:8:2301:15974:162969/2 +GGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACACTTAACCC ++ +;:F3<+<+)88?@:8B*94?9;;B;=@=8@3).8).=7CE=))77?? +@HISEQ1:121:C0EP5ACXX:8:1104:12202:167998/2 +GATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAAC ++ +IJJ@BFGHIIGIIGJJIGEIJIGGHIGHIJIJJJJJGHJJEJIIJJIJGGCECAEHEHHHHEFFFFABEEDCCDCCBBC??BCACDDCCCD?DD??BB>CCA +@HISEQ1:121:C0EP5ACXX:8:1107:6868:53096/2 +GCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCA ++ +JJIIIJJJJJJIJJIJJJJJJJJJGJJJJJJJIJJIJIJIIIJJJJJJJIJJJJJHEHHFFFFFEEDECDDDDCDDDDDDDDDD>CC +@HISEQ1:121:C0EP5ACXX:8:2105:9978:189276/2 +CACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCANNNNN ++ +JJJJJJJJJFHGIJJJJGJJIJJJJIJJJJIIJJHHHIJJJJJJIJJIIJJIJHHHEHDFFFCEEECEDDDDDDDD?CDCCCCDDDC +@HISEQ1:121:C0EP5ACXX:8:1308:18392:2877/2 +ATCAATCTCCAATCACCATGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTANNNN ++ +AHD9CAFDGCE@A?FGEA*9*:1*0*?GCGGHIJJGG34BBFE>A;AGID>EHHHHHHFFFFFFDEEEDEDDDDDCDDDC:@ +@HISEQ1:121:C0EP5ACXX:8:1205:6454:8959/2 +AGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTT ++ +JJJJIIJGGJIJJJIIIJJJJJJIJJGIHHHFDDDDDDDDDDCDDDDDDDDDEDDDDBDDDDEDDDDDDDDDDDDDCDDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:2105:5499:95549/2 +CTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTA ++ +JIIIFIJJIJJJJJJEHHFHHJJGIIIIFCGGJJJHFGHCDHGIIIG>GIJJJIEHHHFFD@CEECEEEC@ABBDBCCBBBBD>BDC +@HISEQ1:121:C0EP5ACXX:8:2303:18227:25094/2 +AGAGGCGAGGAACGAAACTCCTTCAAGAGCGACCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTT ++ +JJJJJJJJJJJJJJJJIIJJJJJJJIJJHHHFFDDDDDDDDDDDDDDDDDDDECDDDBDDDDEDDCDDDDDCDDDDDDDDDECDDDD 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+CTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTT ++ +GJJJJGIGJJCGHHIGJJIIJJJIIJJIGIEEHJJBFGGIEGIGHIJEHGEGIJJJJIHHGHFFFFF@BCCC@CCDCDD@>CCCCC? +@HISEQ1:121:C0EP5ACXX:8:2204:18585:104307/2 +AACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAG ++ +ED>;>>A:@3(5@?CD:@@@C4@A?9008:A3>@:>@(:>C::>:?:ACC@ +@HISEQ1:121:C0EP5ACXX:8:1207:19105:92282/2 +CCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCC ++ +IIIIEHIIHHFICGHIJJIGIHFGIIJJJJIEGIJIBGIIJHHHFHIIIJHJGIACGH;CEHHHDFF>;?CCCCCBBDBBDDDD;@5 +@HISEQ1:121:C0EP5ACXX:8:1301:17377:139560/2 +GCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATAC ++ +GB:FHHEFGE?FEE55:A99@>>>:@>>:93<><@>3>:(:48:>A@CCC?A>A +@HISEQ1:121:C0EP5ACXX:8:2203:19760:174167/2 +GCGAAAACAGAGGCGAGGAACGAAAATCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAAT ++ +CB?6=9(5>CC?>CCCC@CDC(4:9<@C@>::8>@C@:@CCA 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+JJJJJJJJD@BDDDDDEDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCDDDDDBDDDDDDDDB@A3>>@CCCDEC +@HISEQ1:121:C0EP5ACXX:8:2204:9269:145789/2 +CCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATATCTTCACTTGCCTCTTATTTN ++ +CH3?:A;;FG>;9BCB65(,5535;>ACAC?>@C@4>>CD +@HISEQ1:121:C0EP5ACXX:8:2303:12137:88145/2 +CGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTN ++ +IJJJIGIIJD7@BBDDD@CCCDCCCDCDDDDDDDDDCDDDDDDD@DDDDDD>CCDDDDDDDDDDDBDDDCDDDDDDDACACCDDDCC +@HISEQ1:121:C0EP5ACXX:8:2107:6159:66543/2 +TCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCANNNN ++ +GJIJJJJJIJJJIJJIIJIJIJGIJJJIIJIJJJJGBGHIJJJJJGIGJIJIGHGHFHFFFFF@CECCCDDDDDDDDBDDDCDCCCC +@HISEQ1:121:C0EP5ACXX:8:2207:2890:5397/2 +CCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGC ++ +A88388A88>CA>979BDC8AC3?<0;7588+00?>BC4@>CDD>442?>-5-599>:>@C +@HISEQ1:121:C0EP5ACXX:8:1306:11902:61347/2 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+JIJIEG;FGGIIJJEHEHGIJDCB:HGFGHHJJIIJEBD> +@HISEQ1:121:C0EP5ACXX:8:2107:19055:184454/2 +GTAAGCAGAAGAGCATACAAACCTTGGGTTGTGGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGN ++ +HACFH>C+;CCDDDDD@CCC>A>>BBD5>8AC?@DBB@9 +@HISEQ1:121:C0EP5ACXX:8:2306:15081:197220/2 +GCAAAAGAGCATACAAACCTTGGGTTGTGGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAACCAGAGGCGAGNNNNN ++ +A:@CDCA@55<<)8A<28?75<93028< +@HISEQ1:121:C0EP5ACXX:8:1108:18185:47615/2 +CGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCANNNNNNN ++ +FB@HB;CB?E49*)9?FDFECHIG:=8=BDB4=DE;@AE:;=@9;;;;>>C@B?;;?@@>@>>>CC@A@ +@HISEQ1:121:C0EP5ACXX:8:2105:7748:124139/2 +CAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGC ++ +JEGIHB?CCC=?=@5;=B:A@@@AA; +@HISEQ1:121:C0EP5ACXX:8:1201:13322:122364/2 +ACCCCCTATCTCAGATCCGATGCTCGGCGACCTAAAGAGACTGTATTCTTCAGCAACAATCAGATCCCCAGATTGATTTGCTC ++ +IJGIIJGHIE>GHGHEDHHAEH=FG=:;FEGHEHFGDDEBCAACEECEFEDDCDCDDDDDAC@:@:CCDDD?CDA>CCD@CDA 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+IJIJJIIEIJJJJIJIJJIJIIGD:DGGIJIBGIJIHHIJJIDGIHHFHFFDDED=ACDDDCDDDABB'5@@EHFDBD2>>>;>=?>CD35@>:CCDD@ +@HISEQ1:121:C0EP5ACXX:8:1101:11189:44094/2 +ATCCAATTGATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTATAGAATTGAAACAAGAGCCACACCAGGAAAGAGCCTTNNN ++ +JJJJJJJJJJJJIIIJJJJJJJJ?FGIIEHJGJJJIIHHIJJJJJJJJJIJJJJJJIIJJJIHHHHHFFFDDDDDDDBDDDDDDDC> +@HISEQ1:121:C0EP5ACXX:8:1102:2324:141339/2 +AAACCATGAGCGACAATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTATAGAA ++ +JJJJJJJJJJJJIIJJJJJJFHHHIJJJCHIJJJJJJIIJJJJJIIIIJJIJHGGHHH@DBFEECEEEEDD>@DDDDDDDDDDDEDA +@HISEQ1:121:C0EP5ACXX:8:2102:5334:25020/2 +TAATATAGCACAATCATATTGTTGACACCTTGAGTCCACAAGGAAGGCATGTAATGTTAATAAAATTCAAATTATGTAATTTCAGCT ++ +4CFFE@HHEH>F@GHEIJJGGGGECHCHIIJGGIJJFEGIJIIEGHEIIGHAEHHF=ACCBCCDFDEECDEDAC>>@B5;BCCCCCC +@HISEQ1:121:C0EP5ACXX:8:1208:3562:49824/2 +AATCTCAAACCATGAGCGACAATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACT ++ +AFBHIIGGIIGE@C@HIJAHIACCCE?A=ACDCCDDCCCC5>CCDC8ABC 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+@HISEQ1:121:C0EP5ACXX:8:2306:19017:130779/2 +TCAGATCGGTGCTTGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAAT ++ +EHIJFHBGECGHGIIJIIGIJJJJBFGBHJJIJJGIIEGGJJJJIHI>EF?EDEFFFEE>CACEDCCCCCCA?FGAGFIGCHIJJE=FD=FGG@EC@GEHGB@EHHE;;CBEFD>;A/'',:5:?>CC>5:5,:(CEDABDB?BD?@ACADC::ACDAD<@BBD89 +@HISEQ1:121:C0EP5ACXX:8:2301:14772:138623/2 +CTCTTGTTTCAATTCTATAGTTTGTTTACTATTTTCTATAACCCTATGCCTGCATCAATTGGATCTGATAACCTTAACACCTATTGT ++ +JIJJJIIJJJIIIIIJGIHIEIIGGHIGIJJJIJJIGHIGIHIIIIJJIJJIJGGHIIIHJJIJHHHGHFFFFFFFEDEEDDDDDD; +@HISEQ1:121:C0EP5ACXX:8:2306:2564:73699/2 +ATCTTACAACGAAAACAAGGAATGAGATTACTTATAATATACTCGGTAAGACTGAACGCAACACCATATTTCCGGATCCAATCNNNN ++ +II>FHCHGGIBHGEGHGCCD9CDFIGJBFFGGGHIEG;@@CHCGGGHAEE<<@CDCCC@B@B@9ACCCC:C@ +@HISEQ1:121:C0EP5ACXX:8:1303:13585:40340/2 +AATATAGCACAATCATATTGTTGACACCTTGAGTCCACAAGGAAGGCATGTAATGTTAATAAAATTCAAATTATGTAATTTCAGCTT ++ +GHDIGG4ACHGG?EEHIIIB?DCGG9GHGIEGH4DCEDA@DACCCECBBBDCDCDCCDA +@HISEQ1:121:C0EP5ACXX:8:2107:18091:187815/2 +GTTTGTTTACTATTTTCTATAACCCTATGCCTGCATCAATTGGATCTGATAACCTTAACACCTATTGTCGCTCATGGTTTGANNNNN ++ +GIIEG3+FF@HHIJIJJGIJJJJJIIEIIIJJGIGCIIIJGHIJJJJJJJIGGJJJIJJJJGGIIHGGEEFFFFEFFEECEEEDCCCCCCC +@HISEQ1:121:C0EP5ACXX:8:1305:4292:178325/2 +TGCAGAGCAGCAACAAAATTGATTCCAATAATACATCTAATCTTGAGATCCAACATGCACAGTCTCAACTGGAAAGGATCAATTCTA ++ +IJIIIIIEHIJIIIJIJJIGEIGHEGIGIJIJJJIFFGGIHJIJJGBDGIJJJFIJJJEHBEAHHFFFFFCACECBB9@CBDDEDDD +@HISEQ1:121:C0EP5ACXX:8:2201:1091:169035/2 +TGAGNNNNNTTGGATCCGGAAATATGGTGTTGCGTTCAGTCTTACCGAGTATATTATAAGTAATCTCATTCCTTGTTTTCGTTGT ++ +HIGI#####21@EEFFHGHGFHF>FGHHFFHEEI;;@DE@DHHEFHG6?;@CECDDC@ACDDDECC>5>CCCACDDACCCBBDA@ +@HISEQ1:121:C0EP5ACXX:8:2201:15300:19470/2 +TCACAAGGCTTGAGCAAAGGTAGAGGAATCTATCTAACACACTCTCCTGCAGAGCAGCAACAAAATTGATTCCAATAATACATCTAA ++ +JJJGHIJGIIJJHIJJJIJJFHHJIJJJIJJJJJJJHJJJJJJJJIJIIJJJJIIIGHHHHFFFDCEEEEEEFECDDCDEDDCDDDC +@HISEQ1:121:C0EP5ACXX:8:1308:14340:140874/2 +CAGAATAATCACAAGGCTTGAGCAAAGGTAGAGGAATCTATCTAACACACTCTCCTGCAGAGTAGCAACAAAATTGATTCCAATAAT ++ +EEB9EH<3GGG=4@)=D;777C9=?)).7))66=;?A>3(-5;>@>A5@; +@HISEQ1:121:C0EP5ACXX:8:2202:12780:47547/2 +GAATAATCACAAGGCTTGAGCAAAGGTAGAGGAATCTATCTAACACACTCTCCTGCAGAGCAGCAACAAAATTGATTCCAATAAT ++ +GAFGGDHEGH@AC8?FDHAE?EGBG@HGCHEGHCGGBFEGHIGHHGGA@AFGH>HGHEHGEHC?@7@A2;?@:;CDCBB>>5:@C +@HISEQ1:121:C0EP5ACXX:8:2106:13356:92925/2 +TACCGAGTATATTATAAGTAATCTCATTCCTTGTTTTCGTTGTAAGATTAGTTATGTTTCCCTGGCTTATTCTAATCTAGTTAGAAT ++ +JGIJJAGFDHGIHEGIJJGIHGIJJGIJIJIJIGHJHHGHIJIIIIGHIIIGIGGIGIJJHHHHHFFFEFDDDC;CCDDDDEEDDDC +@HISEQ1:121:C0EP5ACXX:8:2206:14713:40562/2 +GATCGGTTTGATTTATTTGATCAAGGATCTTTCCTGGTGTGGCTCTTGTTTCAATTCTATCGTTTGTTTACTATTTTCTAT ++ +FFD@GGBGBGIBFGIIFIB?FFE:=@=.===7?C;;.;CC(;;C?(5>>CCDCDDAD diff -r 000000000000 -r 05c27700e5ca demo_files/mother_male.bam Binary file demo_files/mother_male.bam has changed diff -r 000000000000 -r 05c27700e5ca demo_files/mother_male.bam.bai Binary file demo_files/mother_male.bam.bai has changed diff -r 000000000000 -r 05c27700e5ca demo_files/reference.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/demo_files/reference.fasta Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,19 @@ +>comp0_c0_seq1 +ACAGAATAATCACAAGGCTTGAGCAAAGGTAGAGGAATCTATCTAACACACTCTCCTGCA +GAGCAGCAACAAAATTGATTCCAATAATACATCTAATCTTGAGATCCAACATGCACAGTC +TCAACTGGAAAGGATCAATTCTAACTAGATTAGAATAAGCCAGGGAAACATAACTAATCT +TACAACGAAAACAAGGAATGAGATTACTTATAATATACTCGGTAAGACTGAACGCAACAC +CATATTTCCGGATCCAATCAATCTCAAACCATGAGCGACAATAGGTGTTAAGGTTATCAG +ATCCAATTGATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTATAGAATTGAAACA +AGAGCCACACCAGGAAAGAGCCTTGATCAAATAAATCAAACCGATCTAACCTTGGGTTGT +GGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGA +AACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGA +ATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTC +AATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGC +AGCCTTCAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCA +AGCACCGATCTGAGAACCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAG +GGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCCCCACAATTTGCAAGG +GCAAATTATGTGTTCCACCACAAAATGAAACAAGAAAGGAAAGAAAACAAGCACAGAGGG +GAGGAGCAAAGCTCCATCCTAGGCTTGGAAGAGATTCGAACAAGAACAGAGAAGAAGAGA +GAGGAAACTGTAGAGAGAGGAGAGAGCGTTTTAGAGGAGAGAGGGAAACAGCCCGGATCA +CCAGCTAAGGCCCCT diff -r 000000000000 -r 05c27700e5ca demo_files/reference_male.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/demo_files/reference_male.fasta Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,30 @@ +>comp0_c0_seq1 +GTTCTCCATTCCATTCTAAGTTTGGCAAATAGCCTTGGGAATTCAATGCACTCTCCTACT +AGGAAACCAAGGATTGTGAGTTCCTTCTTTTTTTTTGCTTGGGTTCTAGCAAGAGCAAGT +TTATTAAAGAGAGCTTTGGGATCAAAAGTTTTGGTACCTGATTTGGTCACTTTTGGTTTG +GAACTTTTTGTGCTACCACAAGGTGGTGTGAGATTTGGTAAATTTGGGGAGTTGGTATTC +CCCTTGTTTTGTTGGTAAGCATCATTGATGTTGGTCGTACTATTTTTGGTAGCATCATTA +ATCACCATATCAGCAAAGGAAAGCTTCCCCTTCCCCTTATCCATAGCAACCCTCTCTTCA +GTAAATGCACACACCCACTCACTGTATCTAAAGCTCACTATGAATATTAACCAGTACAGA +GCAGATTTACTCGG +>comp1_c0_seq1 +GTCAATGGTCTCTCTCCTCTAAAACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCT +TCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTTGCTCCTCCCCTCTG +TGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCA +AATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACACTTAACCCTTACTT +TACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCC +CTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCA +CCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCC +TAACTCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTAAAGAGACTGTATTCTTCAG +CAACAATCAGATCCCCAGATTGATTTGCTCTGATGGCCGCTCTTGAAGGAGTTTCGTTCC +TCGCCTCTGTTTTCGCAAGGAGTTATGGACAACCCCCCTTCGTTGCTGGAACCACAACCC +AAGGTTAGATCGGTTTGATTTATTTGATCAAGGCTCTTTCCTGGTGTGGCTCTTGTTTCA +ATTCTATAGTTTGTTTACTATTTTCTATAACCCTATGCCTGCATCAATTGGATCTGATAA +CCTTAACACCTATTGTCGCTCATGGTTTGAGATTGATTGGATCCGGAAATATGGTGTTGC +GTTCAGTCTTACCGAGTATATTATAAGTAATCTCATTCCTTGTTTTCGTTGTAAGATTAG +TTATGTTTCCCTGGCTTATTCTAATCTAGTTAGAATTGATCCTTTCCAGTTGAGACTGTG +CATGTTGGATCTCAAGATTAGATGTATTATTGGAATCAATTTTGTTGCTGCTCTGCAGGA +GAGTGTGTTAGATAGATTCCTCTACCTTTGCTCAAGCCTTGTGATTATTCTGTTGAAGAA +CTTCAGTGATATTCATAGAGTGCATAGTCTTAATTATGACTTTGATAAAGTATTTTCCTT +AGGTTATGAGTATTTCATTTCTAGACTTTATTACCATCTCCTTCGATCTTTGATTTGTAA +GCTGAAATTACATAATTTGAATTTTATTAACATTACATGCCTTCCTTGT diff -r 000000000000 -r 05c27700e5ca demo_files/son.bam Binary file demo_files/son.bam has changed diff -r 000000000000 -r 05c27700e5ca demo_files/son.bam.bai Binary file demo_files/son.bam.bai has changed diff -r 000000000000 -r 05c27700e5ca demo_files/son_1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/demo_files/son_1.fastq Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,392 @@ +@HISEQ1:121:C0EP5ACXX:8:1204:18279:146920/1 +CTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTC ++ +JIHIGGGJIJJGIIJHJJJJIJHIGIIIIGJGIJJIGIIIIIJIIBHCCHIJJIEIJJIHHFEHFFFFFEEEEDDDDCDC>ADDD?= +@HISEQ1:121:C0EP5ACXX:8:2304:5972:188977/1 +TACGGGGCGAATCCCCACAATTTGCAAGGGCAAATTATGTGTTCCACCACAAAATGAAACAAGAAAGGAAAGAAAACAAGCACAGAG ++ +IIJJJJJIJJJJJJJJEGIGJJJJIHHHHHFFFEEEEEEDFBDDDEDDDDDDDDDDDDDDDDDDDDDDBCDDDDD?DDDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:2304:17680:15723/1 +ATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACAATTTGCCCTTGCAANNNN ++ +JIJJJJJGJJIJIJIGIJJJJJIIIGIJJIIJJJJJJJJIIIIGIIJIJJGIJJJJIIJHEADFFFFEDDEEDACDDDDCDDDDDDC +@HISEQ1:121:C0EP5ACXX:8:1306:15258:144587/1 +ATGGGTAAAGTTTTGGGTATACGGGGCGAATCACCACAATTTGCAAGGGCAAATTATGTGTTCCACCACAAAATGAAACAAGANNNN ++ +FBGCGAFHIHHHIIIJI;EFIEIIJIIJBEHFHDDDECCEEEEED@CDDBB@>AAAA +@HISEQ1:121:C0EP5ACXX:8:1106:16812:199346/1 +CCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTG ++ +FGGGIGIIIEGEHHCCBCGHHECGGIIIIFGGHE??GHIIE@FH2BFGGIGIADGE@@EHHHFEDDDFECECCCCCCCCCCBBCBA: +@HISEQ1:121:C0EP5ACXX:8:2207:14699:5997/1 +TTATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACACTTAAC ++ +JJJJJIJIGJJHHHJJGGHHIJJFIJGIJJJJJJIJGJJGGIJIJHGHJEIHHFF>BECEDDDBDDDDDDDDDDDDDDDDDDCDDDD +@HISEQ1:121:C0EP5ACXX:8:1308:15728:74115/1 +GCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCCCCACN ++ +GGGIJIIIJIGIJIGGIHFJGICHIIBG9BFHIGGEGGIDHIEICDEHJIJJHH?EEFFFFBDEDDBCCDEBDBDDDDBDDACBCD? +@HISEQ1:121:C0EP5ACXX:8:2104:4107:189035/1 +CTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTC ++ +IIJIJJJJJIJJJIJJJJJJIIJJJJHJJIIHGIIJJJJJJIIJJFHIJHJJJIIGGHGHHHHFFFFFFDDECDDDDCDC>CCDD?= +@HISEQ1:121:C0EP5ACXX:8:1303:8466:21687/1 +GCACCGATCTGAGAACCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTTATGGGTAAAGTTTTGG ++ +JJJJIJIJIJJIIJJJJJJJJGIIIJIIIGIJ@EGHACHFFFDCDEECFDCDEEDCACCDDDBBDDDD@DCCDDDDCCAACCCDDDB +@HISEQ1:121:C0EP5ACXX:8:1301:5823:42774/1 +GCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTT ++ +JIJJJJJIJJJIIIJIIJIIIJGGIJJJJJIJJHHHHHFFFDEEEDDDDDDDDDDDDDDDDCCDDEDCDEECCCDDDD?ABDC>CC@ +@HISEQ1:121:C0EP5ACXX:8:1205:8107:84323/1 +CAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAAAATCGNNNN ++ +JGIJJJJJJJJGGIJJJJIIJIJJJGIIIJJJIJJIJIIIJGHJHFFFFECCDDDDDBDBB@>CCDDDDDDDBDBDC2@CCA@@A;9>BB9; +@HISEQ1:121:C0EP5ACXX:8:2302:9661:103451/1 +CAGCCTTCAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCN ++ +JJJIIIJJJJJJJIJJIJJIIJIGIJIHIIIJJJJJIIJJJIJJHHGHFDFDDDDDDDDDDBBDDDDDBDDDDDDDDDDDDDD?BDD +@HISEQ1:121:C0EP5ACXX:8:1203:11100:134680/1 +AGAGCAGCCTTCAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGG ++ +AGHJJIJJJJJJJJJJJJFIJJJGGJJJJJJIJJJJJJJJIJIIIJHGHFFFFDDDDDDDDBBBD@BDDDDDDDDDDDDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:1204:11305:110710/1 +CCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTG ++ +JJJJJJJJJJJJJIJIJJGHIJIJJJJJJJJJJIIJJJJJJJJIJIJJIIIJGIGIHJHHGHHFFFFFEEDECCCDDDDDDDDDDDC +@HISEQ1:121:C0EP5ACXX:8:2104:4236:84531/1 +TCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCC ++ +GHIIIIAHFH;FBCBFFH?>?GA@BB<*?F<9DGIEHBF?BBDHII9FEGH@@@@D7@;CC;AAB77;;@CAA?7>C59BB?B?BDDD +@HISEQ1:121:C0EP5ACXX:8:2101:6432:199800/1 +GAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTTCAATCAATCTCCAATCACCATTCGNN ++ +B?AF@FHDCA9A2A;>@>CA@CACCAC(5:;@:5 +@HISEQ1:121:C0EP5ACXX:8:2107:18331:159767/1 +GAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTTCAATCAATCTCCAATCACCATTCGCN ++ +JIJJIGIIIJJJHEFGHIJIJJJJJJIJIJIJIJDGIHIHIFHGIJJJ@EGIIHEHEBEDFDCEDDEEDCC;ACDDDDDCDDDECB9 +@HISEQ1:121:C0EP5ACXX:8:2306:3755:139456/1 +GCCCTTGCAAATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCT ++ +EHHHJEGIJJIGIIEHIGICEHBFHED@@AH>CEFFHIJIJHGHHFEFFFF@BCCCCE@CDCDDDDDCDEDCCDCCDEECDDCCCDC +@HISEQ1:121:C0EP5ACXX:8:1307:2138:123308/1 +AACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGG ++ +IIJJJIIIIGIDHHI>FEHIIIIJJJGJJJJIGGIEHIJICGHGIGGIIJJJJIJFCGEEC=BDEFFB>>CCCC@CCCDD??BDDCB +@HISEQ1:121:C0EP5ACXX:8:2202:11183:23671/1 +TACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGNN ++ +JIIGIHJIJJJJIJJIGIIIIIBFGIJJJJJIIIJIGDGHIHJGICHIF;FEEHGFHFHHFFEFFECBACC@CCDCBC +@HISEQ1:121:C0EP5ACXX:8:1304:1821:110599/1 +CTGAGTTAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTACAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAG ++ +@EEF@+A??FEEG?FGFCFGAHGBCDHIHIII=CHEDBEB@>>>@6>3;CC(;ACACCC>>AAB@??C>>CCCB3>C>>AB59<8@> +@HISEQ1:121:C0EP5ACXX:8:1202:6596:74809/1 +CCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAG ++ +JIJGIJJIJJJGIJIJEIEGGIIJJJ:AE>D?@CCEECEDCDACEDDEDBDDDCC>CDDDDDDDCDCCCCDDCDDDDDDD>A@CCD8 +@HISEQ1:121:C0EP5ACXX:8:2305:7769:151169/1 +TCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGTGGGGATTCGCCCCGTAT ++ +JJJJHIJJIJJJJJJJJIIGGIJIGCHHHIJIJIFJJIIIFFHIIIJGGGIIIJJGIJIHHHGHFFFFFFFCDDDBDCDDDDDD@BA +@HISEQ1:121:C0EP5ACXX:8:1205:2077:37536/1 +AAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGAC ++ +IJJIJGCGCEHFGIH@EHIJGEHIIJEGIBIJIJCEGCGAGCCEFDCDD9;?5>:A>ACDCACDDBAC>BA>@:@>?@C4@A +@HISEQ1:121:C0EP5ACXX:8:2103:4295:63104/1 +TCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGG ++ +HGGGHEAHEHIHIIIGHIHGHIHGIEIIGIIIIIIIIIIIGI=FGIIIEGHGGIIIIEEHHEECEBDDDCABCDC?CADCACAB<>: +@HISEQ1:121:C0EP5ACXX:8:1103:4347:43083/1 +AACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGG ++ +JJJJJJJJJJIJJJJGJJJJJJJJJJJJJJJJJJJIJIJJJJJJJJJIHIJIJJJJJJHHHHFFFDDDCCEECEDDDDDDBBBDDD@ +@HISEQ1:121:C0EP5ACXX:8:2107:17275:98920/1 +TGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCC ++ +JDGIJJJJIJJGIJJJJJJIGJIIJJJJJJIJIJIIGCFCGIIIJHHCHHFFFFFFFEDCEDDDCDDDDDBDDDDDDECDDCCACD9 +@HISEQ1:121:C0EP5ACXX:8:2304:10198:198268/1 +GGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAG ++ +JJJJJJJJJJJJJJJJJJJIHIJJJGHIIJIJHIIJJJIJJIIJIIJJJHGGHHFFFFDCD?CDDEDDEDDDDDDDDDDDDEEDCCC +@HISEQ1:121:C0EP5ACXX:8:1205:11549:169371/1 +TACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGGGCTCCTCTGCTCCCT ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJIJJJJIJJJHHIJIJJIJJIIEGHHHHFFFFFEEEDEDDDDDDDDDDDDDDDD? +@HISEQ1:121:C0EP5ACXX:8:1307:11095:87598/1 +GAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGN ++ +IJJJIIIJJJJIIIJIGIIFGGIIJIJJIJIIIIJJIIGHGHJJGHGFHFFFFFFCDECDECDDDCDDDDDDBDDDDDD?B@CD@C> +@HISEQ1:121:C0EP5ACXX:8:1307:5273:167214/1 +CCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTG ++ +JIIIJJJJJJJJFIIJJJJJJJJJJJJJBGIIJJGGIGGIIJJJIJIJIHHHHHFFFFFEDCDDDDDDECDDDDDDDDDDDDDDEEE +@HISEQ1:121:C0EP5ACXX:8:1202:6430:193858/1 +AAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGN ++ +JJHIJJJJJJIJJJJJJJJJJJJJJJJJJJJJIIJJJJIJJJJHHHHHHFFFFFFEEFEEEDDDDDDDDDDDDDDDDDDDD?BBDD: +@HISEQ1:121:C0EP5ACXX:8:1203:11801:61902/1 +AAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGN ++ +JJJJJJJJJJJJJJJIJGIIJJJJJJIJJJJJIIJJJIJJJJEHHHHHHFFFFFFEECEEECDDDDDCCDDDDDDDDDDDDBDDCD> +@HISEQ1:121:C0EP5ACXX:8:1108:8809:81311/1 +TCGGTGCTTGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTT ++ +JJJBGHIJGGEHIGGGJJJIIJJIJJJJJIIJJIIJJJIIJJJJICHHHHHFDF@DCEEEDCDCDA?@A8@CDDCCDBBBBDDCCD> +@HISEQ1:121:C0EP5ACXX:8:2204:18606:175884/1 +GCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTC ++ +:FDEBHGIBHI@GEEFBGEEFDDDC>ACEC@ACB?B@@?@AC@CAC@C>ACCCDDC +@HISEQ1:121:C0EP5ACXX:8:1105:17367:119872/1 +TGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCC ++ +IJIJIJJJIJJIIJJJIJJGIIJJIJJJIJJIBHIJJ@FCIJJJJHHHHHFFFFFFFEDEEBDDCDDDDDDDDDDDDE@CDCCDDD> +@HISEQ1:121:C0EP5ACXX:8:2202:9681:198266/1 +AACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTG ++ +DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCCDCEDDD@BF@EFAEHEHCGHIIIBHGGI>>BGGHH@DHBBFDHIG:CD@GECD=CCEAEE>B;?B=BCCCC?>;AA::8>8>38>AA>AA799::A=3+328::859:>:+8>?7&5>((+4>49AA3>: +@HISEQ1:121:C0EP5ACXX:8:2207:13105:76511/1 +TGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTC ++ +IIIIJGICHGIJJJJEHEGGGHIHGGEGCHIJJJIJIJ<@BFDFHIJEGGEGHHGGHA;>?DDDCCEDEDDDCCDDDDDDD<<@ACC +@HISEQ1:121:C0EP5ACXX:8:1306:20726:15789/1 +GAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATTTTGTGGTGGAACACATAATTTGCCCTTGCAAATTGT ++ +A:CA4=DC=?=6;?;;6;;;;BBAABBA955:>AB>>; +@HISEQ1:121:C0EP5ACXX:8:2107:15019:37435/1 +CCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCANNN ++ +IJIJJDIGIJJJIJIID0:@7CDDEDDDDDDDDCCDDDDDDDDDDDDDBDDBDBDDDD->AAACDDD:ABDDDBDDDDCCACDCDC@ +@HISEQ1:121:C0EP5ACXX:8:2208:13905:97948/1 +GCCCTTGCAAATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCT ++ +AGHIJJJJJJJIJJIJGIIGIGJGIJIJJHIIJJJJJJJJJHHHHHHFFFFFF@A(>ACCDDDDAC@ADCCCDDDCDEECCDDDDCC +@HISEQ1:121:C0EP5ACXX:8:1301:2094:147266/1 +GGTTGTGGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCAT ++ +JJHIIIIJGGIJJJJJJJIJJJIIIJD076:CDDDDDDDDDDDDDDDDDDDDCDCDBDBBDBBDDBBDBCCDDDDDC@CBDDDDDDC +@HISEQ1:121:C0EP5ACXX:8:1306:10553:20592/1 +GGTTGTGGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCAT ++ +JJGHIIIIGIJJIJIJIJIJJJIJIJD@BDDDDDEDDDDDDDDDDDDDDDDDDDDDDDDDDDBDDDDDDDD@CDDDDCDBDDDDDDC +@HISEQ1:121:C0EP5ACXX:8:1203:5698:36196/1 +AGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCC ++ +IIIII>CEFFHIGBCCBEGFHCHBFDFHICDHHGICBHEGB@HGICE;FCH:DAE@AEH3=?CDD@DECCED;CCDA:>A:A? +@HISEQ1:121:C0EP5ACXX:8:1107:20608:196329/1 +TTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCC ++ +IJJJJJJJJJJIIJJJIJJJJJJJGHIJJIIIJJFJIIJIIJJIJJIHIHGEIJIG@EHGCAEFDDCEFDDDC>A:?@@CCC<5 +@HISEQ1:121:C0EP5ACXX:8:1104:7384:82234/1 +ACTATAGAATTGAAACAAGAGCCACACCAGGAAAGAGCCTTGATCAAATAAATCAAACCGATCTAACCTTGGGTTGTGGTTCCAGCN ++ +JJJJJIJJJJIIIJJIJIJJJIJJJJGIIIJIJJJHJIJJIJJIJJJJIJJJJJIIJHHHFFDEEDDDDDDDD?BDDBD?BCDEDDD +@HISEQ1:121:C0EP5ACXX:8:1106:13934:41628/1 +TTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTG ++ +JIJGGHJGFGHIIJJJGF6??FGBGGGIJJIJIIIJJIJJGEEEHHFFFFFDDC@CACA5;;;CCDD@@CACDCDDACCD?CCDCD5 +@HISEQ1:121:C0EP5ACXX:8:1203:15133:98209/1 +TTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTC ++ +JJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJCHIIJJJIHIJJJJJJJIJBHIJICHEIHHHHHFFFFFEEEEEEDD??BDDCDDDC +@HISEQ1:121:C0EP5ACXX:8:2201:15934:79822/1 +ATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTATAGAATTGAAACAAGAGCCACACCAGGAAAGAGCCTTGATCAAATANNN ++ +HIJJIIJJHIHIJJJJIIIIJJCHIJIFIIJJGIJJIGIIJJJJJJJIJJJJJJJJJJJJHEHFFFFEBDEEDDDDDDDEDDDDCDE +@HISEQ1:121:C0EP5ACXX:8:2103:11160:152496/1 +CAATTGATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTATAGAATTGAAACAAGAGCCACACCAGGAAAGAGCCTTGATCNN ++ +IIIIEIIIEGBEEGGDGHIIFHIIIIIIGGHIGFFEGHIIIIIFIIIIIIIIIIIIIIIGGEEEHHEFFCCCEC?ACCBCCCCCCDC +@HISEQ1:121:C0EP5ACXX:8:2205:18696:101935/1 +TTCTCAGATCGGTGCTTGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGG ++ +HHGFGEEDHHIDHDGIIJIIJ@FGGJIIJDIJIGHGIGGIIJJEIIJJGHE9;7?BBCCCE>@CDD@C@>>CA>9@B<@A@C:@B?< +@HISEQ1:121:C0EP5ACXX:8:1205:12485:13377/1 +CTATCTCAGATCCGATGCTCGGCGACCTAAAGAGACTGTATTCTTCAGCAACAATCAGATCCCCAGATTGATTTGCTCTGATGGCCG ++ +JJJJJJJJJJJJJJJJIJJJJJIJJJJJJJJJHHHHHFDFFFFFEEEEEEDDDDDDDDDDDDDDDDDDDDDEDEDDDDDDDEDDDD@ +@HISEQ1:121:C0EP5ACXX:8:1205:4852:183027/1 +GCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGGTGCTCTCACCGGAATCTCTTCACTT ++ +AEA?AA+3+@:1?C?D49??B;0:*09?AAA +@HISEQ1:121:C0EP5ACXX:8:2105:10921:73090/1 +TCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCAGATCCGATGCTCG ++ +JJJJJJJJJJJJJJJJJJJJJJJJHIFHIJJJJJIJIJJJJJJIIIJGIJJJJHHHHHFFFFFEDDDDDDDDDDDDDDDDDDDDDDB +@HISEQ1:121:C0EP5ACXX:8:1301:9478:45031/1 +ATGAGCGACAATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTATAGAATTGNN ++ +@FDHIGGIIEIIIII*?F8BGGHGHGIEGHG>F@DG@FHA;>BBACC;@ACCCC@:@ +@HISEQ1:121:C0EP5ACXX:8:2104:6749:159109/1 +AAGGAGTTTCGTTCCTCGCCTCTGTTTTCGCAAGGAGTTATGGACAACCCCCCTTCGTTGCTGGAACCACAACCCAAGGTTAGATCG ++ +HHGHIIFGEHIIEBDAF<@GGIIG?BD>=@A<8AD=E=A=;AB>@BB=AC@BB=?<:@C?CABB?B2<@BB<<<4>CB:@CA +@HISEQ1:121:C0EP5ACXX:8:2202:21245:113808/1 +AAACCATGAGCGACAATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTATAGNN ++ +JJJJJJJDHJJGGIJJIJIIBFGHIGGHBGGCCCDDDDDDCCCC@ +@HISEQ1:121:C0EP5ACXX:8:2206:14046:3125/1 +ATCTCAAACCATGAGCGACAATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTN ++ +JJIJJJJJJJJJGIJIJJJJJJIJJ?DDGHIIJFHIJIJJJIJJJJJIGFHHHHHFFFFCDCEEDDDEDDDDDDDC>BDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:2105:15155:69832/1 +AACACCATATTTCCGGATCCAATCAATCTCAAACCATGAGCGACAATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGCATAGG ++ +IIJIJIJJIJJIJJJGHIJJIIJJIJGGGIGIIJJJJJJJJJJFEBFFFF6>ACEEDDCDDDCDEDDDDDDDDCDEDDDDDDBDCDD +@HISEQ1:121:C0EP5ACXX:8:2302:1358:92768/1 +CCAGATTGATTTGCTCTGATGGCCGCTCTTGAAGGAGTTTCGTTCCTCGCCTCTGTTTTCGCAAGGAGTTATGGACAACCCCCCTTC ++ +HFBEGHIG>HHDGCCFFH@FC>DFEBEFHH3?BFGB@HIE@AC=@CA;<==8B7;.;A@@>>/8??2?3>@>AA3:A88?<<>>9?A +@HISEQ1:121:C0EP5ACXX:8:2302:13383:122517/1 +ACTTATAATATACTCGGTAAGACTGAACGCAACACCATATTTCCGGATCCAATCAATCTCAAACCATGAGCGACAATAGGTGTTAAG ++ +IJJJJJJJJJJJJJJJJHIJJJJJJJJJJIIJJJJJJIJJJJJJJIIJHHHHHFFFFFFEEEEEDDDDDDDDDDDBDDDD:@ABCCC +@HISEQ1:121:C0EP5ACXX:8:1305:19207:34291/1 +CTCATGGTTTGAGATTGATTGGATCCGGAAATATGGTGTTGCGTTCAGTCTTACCGAGTATATTATAAGTAATCTCATTCCTTGTTT ++ +GBGIIIIAFHG4?GFEG;>@;CA@B>;@5>::ADDE@AC3@C +@HISEQ1:121:C0EP5ACXX:8:2102:10551:119670/1 +CGAAAACAAGGAATGAGATTACTTATAATATACTCGGTAAGACTGAACGCAACACCATATTTCCGGATCCAATCAATCTCAAACCAT ++ +JJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJHIIJJJJIJJJJJJHHHFFFEEEEEFDDDDDDDDDDDDDDDDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:1208:7778:129322/1 +TTAGATCGGTTTGATTTATTTGATCAAGGCTCTTTCCTGGTGTGGCTCTTGTTTCAATTCTATAGTTTGTTTACTATTTTCTATAAC ++ +BGHGHIGGEFGIEC@@C;(5;BDDCCCC;@CC +@HISEQ1:121:C0EP5ACXX:8:2304:6605:62458/1 +TGAGATTGATTGGATCCGGAAATATGGTGTTGCGTTCAGTCTTACCGAGTATATTATAAGTAATCTCATTCCTTGTTTTCGTTGTNN ++ +DHHHAH4A@FGIIGIIICAHBC>>>>>@;@@CDEDDCCCCCC?>8<>? +@HISEQ1:121:C0EP5ACXX:8:2106:13776:157073/1 +TCTTACAACGAAAACAAGGAATGAGATTACTTATAATATACTCGGTAAGACTGAACGCAACACCATATTTCCGGATCCAATCAATCT ++ +JJJJJJJJJIJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJIGIJIJJJJJJHHHFFDECDDDDDEEEEDDDDDDDDDDDDDDC +@HISEQ1:121:C0EP5ACXX:8:2306:4709:158183/1 +ATCTTACAACGAAAACAAGGAATGAGATTACTTATAATATACTCGGTAAGACTGAACGCAACACCATATTTCCGGATCCAATCNNNN ++ +IJEIJIIJJJJJIHHIJIIIIIIJGHFHIHIIIJJGIGIJJIJJJJGIDHIGIGIHHGHDEDEC@BCCDEDDC?@BDDDCCCDDDDD +@HISEQ1:121:C0EP5ACXX:8:1104:17239:160204/1 +AGATCGGTTTGATTTATTTGATCAAGGCTCTTTCCTGGTGTGGCTCTTGTTTCAATTCTATAGTTTGTTTACTATTTTCTATAACCC ++ +C@FGABD?@GHIBGI;@@;@C5>>;55@A? +@HISEQ1:121:C0EP5ACXX:8:1207:17351:77865/1 +TTTGTTTACTATTTTCTATAACCCTATGCCTGCATCAATTGGATCTGATAACCTTAACACCTATTGTCGCTCATGGTTTGAGNNNNN ++ +IIIIJJIJJGHGHIJIIIIIJIIJIJIGIJIGIJJJIGIGIFIIJIIGIIJJJEIJJJJJJJIJIIJHHEEEBFFECEBDCB?CCC> +@HISEQ1:121:C0EP5ACXX:8:1204:17042:185305/1 +CAACATGCACAGTCTCAACTGGAAAGGATCAATTCTAACTAGATTAGAATAAGCCAGGGAAACATAACTAATCTTACAACGAAAAC ++ +GE@@D?@GCEHI?F>DE@FHFGGGG>BFHGCEGBFGEGHHF?FB>CHGBGH@HGGGHGGEAEFCD@CEECCCC:;>@CCCB@BBBC +@HISEQ1:121:C0EP5ACXX:8:2103:20915:142998/1 +GAAGGAGATGGTAATAAAGTCTAGAAATGAAATACTCATAACCTAAGGAAAATACTTTATCAAAGTCATAATTAAGACTATGCACTC ++ +GIIII@GGIGIE?FHHIGI?BFHIIIEAFICFGGHGGIIDDGGD@@F@GIIDDHIIIIBAG7=;A?CEHD>CDEC>@>A;3;ADDC> +@HISEQ1:121:C0EP5ACXX:8:1104:9804:126592/1 +TTCTATAACCCTATGCCTGCATCAATTGGATCTGATAACCTTAACACCTATTGTCGCTCATGGTTTTAGATTGATTGGATCCGGANN ++ +IJJIIJJJJJJJJJFJJJIIJJJJJJJJJIJJJJJJJJJJJIJJJJJJIJIJJIJJJJJIHEEAEHFFFFFEEEEEEDDCDCDDBDB +@HISEQ1:121:C0EP5ACXX:8:1302:12570:27266/1 +GGTTTGAGATTGATTGGATCCGGAAATATGGTGTTGCGTTCAGTCTTACCGAGTATATTATAAGTAATCTCATTCCTTGTTTTCGTT ++ +IICFHHIG;HEB@FFGGDEGHIIAHIIGIGCBF?;CEHAGGDG=D@EHHHGDE;@CFDD@CADC>CDDDCDCC@CCCDCDCDDDBD9 +@HISEQ1:121:C0EP5ACXX:8:2108:15621:6710/1 +GTTGGATCTCAAGATTAGATGTATTATTGGAATCAATTTTGTTGCTGCTCTGCAGGAGAGTGTGTTAGATAGATTCCTCTACCTTTG ++ +JIJJJHJJJJJIJHIIIJJIJIIJJIJJ9DFHJJJJJJJFIHIJJJJJJJJJJJJJGHFH@>CEHHFHGHFFFFFFFDEC@CEDDDC +@HISEQ1:121:C0EP5ACXX:8:1204:13269:156814/1 +CACTGAAGTTCTTCAACAGAATAATCACAAGGCTTGAGCAAAGGTAGAGGAATCTATCTAACACACTCTCCTGCAGAGCAGCAACNN ++ +JJJJJJJJHIIJIJJIJJJJIJJJIJGIJJJIJJJJJJJJHIJH?FHIJJGIJIIFEIJIJHHHHHHFFFFDEEDEEBCDDDDCDBB +@HISEQ1:121:C0EP5ACXX:8:2302:20345:190085/1 +ACAAGGAAGGCATGTAATGTTAATAAAATTCAAATTATGTAATTTCAGCTTACAAATCAAAGATCGAAGGAGATGGTAATAAAGTCT ++ +FBGIIEGGFA8CFGGGFFF?B@FGIEEGIIIFIIEDFIEEA@@;DE7?ADDD?B@BCDBDBBBBBB; +@HISEQ1:121:C0EP5ACXX:8:1207:17701:88729/1 +GTAGGAACTCACAATCCTTGGTTTCCTAGTAGGAGAGTGCATTGAATTCCCAAGGCTATTTGCCAAACTTAGAATGGAATGGAGAAC ++ +G*?GHGIGGIJJDHIJJJGHGBFGHIJ;F=F>G@GII=AEHHHGFFFFECACCAABAACCDEDDACCDDCDDDDCCD@@>>@>A>AC +@HISEQ1:121:C0EP5ACXX:8:2104:7678:122935/1 +GCTAGAACCCAAGCAAAAAAAAAAGAAGGAACTCACAATCCTTGGTTTCCTAGTAGGAGAGTGCATTGAATTCCCAAGGCTATTTGC ++ +CGHIEIJIIJDGIGGGGIJJGIJIGGIDCEHHEFEEFDFE@CECC>ABDCCDD5>>@>>??AAC@CDCC:C>ACC>??BBDDDDE>@ +@HISEQ1:121:C0EP5ACXX:8:2205:8175:94899/1 +TTGCTCTTGCTAGAACCCAAGCAAAAAAAAAGAAGGAACTCACAATCCTTGGTTTCCTAGTAGGAGCGTGCATTGAATTCCCAAGGC ++ +:A:ACFHEIDEFHBEHA@D=EEFEEGEEFIIIECE@;=CEEDDD3@A@B:@AA?BAB?B< +@HISEQ1:121:C0EP5ACXX:8:1303:8608:152316/1 +GCCATTGCTTAAGGAGTAAGAGTTGGCTAAATATATGGTAGGGCCTAGCATCCCACACTCTATTAAAATCCACATGGTTTGAGANNN ++ +IJJIJJJJJJJJJJGIGIIJJJHIJJJJIJJJGIHJJJHIJJJIJJJJJJJJJHHHHFFFFFCEEEEEEDDDDDDDDDDDDCDBDDC +@HISEQ1:121:C0EP5ACXX:8:2303:19934:33517/1 +AAGTTTGGCAAAAAGCCTTGGGAACTCAATGCACTCCCCAACAAGGAAGCCAAGGATTGTGAGTTCCTTCTTTTTTTTTTGCTTGGG ++ +GDHFHIJJIIHGEHGJJIJIICFGHIGHIJJJHIJJGJJIIJIGIJGDHJJIJIHCHFGFFED@CEEEECCEDDDDDDDD9@CC@B< +@HISEQ1:121:C0EP5ACXX:8:2206:6805:118993/1 +GGGAAGCTTTCCTTTGCTGATATGGTGATTAATGATGCTACCAAAAATAGTACGACCAACATCAATGATGCTTACCAACAAAACAAG ++ +D?@:FFB@EGHEHAHGGEFHG>FGH*???DDBHBHAHHICFFHGE@F@@CEGHGHE8BCC@CCCCCACCACC@CCCCCBBAB?A?BC +@HISEQ1:121:C0EP5ACXX:8:1302:7919:98849/1 +ACGTCTATTTCCCTGACAAAGAATTATCAAATCCTTGATCTGTCTGAGGCTGTGTCCTGTCTAAAGGGTGTAAGTGTGAATTGCTAT ++ +GHJGEHGHIIJJJJIGGGIGFDGGJGFIGGBBGIFGHGGHIHGHBD=CFHHGHGHGGHIEHEEHHFFFDC9C@C;A>CADDDCCDE> +@HISEQ1:121:C0EP5ACXX:8:2306:12186:45722/1 +ATCACCATATCAGCAAAAGAAAGCTTCCCCTTCCCCTTATCCATAGCAACCCTCTCTTCAGTAAATGCACACACCCACTCACTGTAT ++ +JJJJJJIJIJJJJIJJJJIIIIJIJJJJJJJJJJJJJJJJHIIJJJIIJJJJIIJJHHHHFHFFFFFFFEEEDDDBDDDDDDDDAD@ diff -r 000000000000 -r 05c27700e5ca demo_files/son_2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/demo_files/son_2.fastq Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,392 @@ +@HISEQ1:121:C0EP5ACXX:8:1204:18279:146920/2 +ACGGGGCGAATCCCCACAATTTGCAAGGGCAAATTATGTGTTCCACCACAAAATGAAACAAGAAAGGAAAGAAAACAAGCACAGAGN ++ +IJJJIJIJIJJJJIJIIJJIIGIJJHHHHFFFFEEEDEEEDDDDDDDDDDBDDDDDDDDDDDDDDDDDDCDDBCDDDDDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:2304:5972:188977/2 +GCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTC ++ +JJIIIJIJJFGIJIJJIJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJDIJJJJJJHGFFHHFFFFDEDCACBDDDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:2304:17680:15723/2 +AAGTTTTGGGTATACGGGGCGAATCCCCACAATTTGCAAGGGCAAATTGTGTTCCACCACAAAATGAAACAAGAAAGGAAAN ++ +3CI,CJ;3-=?B@8?CCDCD?CDDEDDDDBBDDCDDCDDDDDCDDCBD?C? +@HISEQ1:121:C0EP5ACXX:8:1306:15258:144587/2 +TCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCTTTCCTTTCTTGTTTCATT ++ +JJJJGFHIIBHJIJIJJJJJIIGICHIJJGHCHGJJGIIIJJJJJIIJJJJIHDHIGHEHHGHEFFFEEEDEEEEDDDDDCCDDDDC +@HISEQ1:121:C0EP5ACXX:8:2201:13125:125595/2 +TATACCCAAAACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCCTGGCCCCGTCTACAGTTTCCTCTCTCT ++ +)1CFCDGG?>EA:BD3@C>A(,;'8(5,55@;>;A@C>C>>A +@HISEQ1:121:C0EP5ACXX:8:1106:16812:199346/2 +CGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCCCCACAATTTGCAA ++ +BHJJHGCF;EGGE?D?CFIAFF@DGFFEBDH?DGGHG=8BBBFDGCFEHEC7@;EHBD,;;;>@;>>?9ACCCA> +@HISEQ1:121:C0EP5ACXX:8:2207:14699:5997/2 +CGAAAGAGAGGCAATAATTGCAAAGGAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCCCCACAATTTGCAA ++ +>2+A+BCHH@)111*?1C?:**0*0)0996D(..8BFF=C;=C;)B.==?>?EEEFFF=CEEDEDDDDDDDBDDDDC>B?@CDDDEA +@HISEQ1:121:C0EP5ACXX:8:1308:15728:74115/2 +CAGTTTCCTCTCTCTTCTTCTCTGTGCTTGATCGAATCTCTTCCAAGCCTAGGACGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTT ++ +GGB?CBFJCEC;3CAECADE>GBCC*:41:)1:B?D?DGGEHIGAFHI6=CC6ACCCBB??ACCCCDDDDC99 +@HISEQ1:121:C0EP5ACXX:8:2104:4107:189035/2 +CCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAGGGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAAT ++ +JIJJJJHIFGIJIJJJJIJJJIIGIHIHIJIJJIJHHEGIGIIJIHAHFEFCEDEDCEEED;@CCDCCDDDDB5:ADDBDDDDBDDD +@HISEQ1:121:C0EP5ACXX:8:1303:8466:21687/2 +AAAACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGC ++ +JJIJGJJIJIIJJJJJJJJJJGJJJGHIGHIJJJJIHIJJIJJJJIHGIJJJJJJIGIJHHHHHHD>CDFCECEEDDDBDDDDDDCC +@HISEQ1:121:C0EP5ACXX:8:1301:5823:42774/2 +AACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTNNNN ++ +JJJIJJJJJJJJJJIJJJIJJHIFHIIJJJJJJJIJJJJIJJJIJJIGJJJJGGEHIJJHHHAE>DFFFE@CEEEDB>ACBDDACCC +@HISEQ1:121:C0EP5ACXX:8:1205:8107:84323/2 +ACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGT ++ +IJJJIJIJJJJJJJJJJJJJJJJJJJJJJJJJIIHIHIJJJJJJJJJJJJIIGHJJJJHGHHHFFFFCEEDEEEDDDBBBBDDDDBD +@HISEQ1:121:C0EP5ACXX:8:2106:8569:128338/2 +CAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCAAANNNNN ++ +JJJJJJJJJIJJJJJJJJGGHJIJIJIJJIJJJIJJIEHHIIJIJCEEF>CCCEBDDDDDDDDDDDDCCCCDCD@BADDDDDCDDDB +@HISEQ1:121:C0EP5ACXX:8:1108:20926:160732/2 +CTTCAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCAAGCACCGATCTGAGAACCTGGGAGCA ++ +HE>BA4AEHIJICGIGCFGGGEIGII9@?CCACD>A(2EHIGAHIIGECACCHFDDFDDADDDBBBBBDB??C89>BDDCDDCD@BCDAB +@HISEQ1:121:C0EP5ACXX:8:1306:11626:15200/2 +GCCCTTGCAAATTGTGGGGATTCGCCCCGTATACCCAAAACTTTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCT ++ +GGFFHGBFGHEHI@FHGEGGGG@FFGHHIAG@HGAF@CHIHHHHFFF?CDFDDCEDC@>A>AABDDDDDE:>C@:ACDDDCDDCDDD +@HISEQ1:121:C0EP5ACXX:8:2101:6432:199800/2 +TCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGN ++ +E?DGGEHG@GCAHGF>FFHHGCHD?FFGC@D)7=CCCHHFFDFAAAACCBCBCA@CDDFGEGDHHD@GII9FGHGIJJ>AFHI@DGGIH@ACCECE@CDDDDDC@CDBD +@HISEQ1:121:C0EP5ACXX:8:1307:2138:123308/2 +CAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTTCAATCAATCTCCAATCACC ++ +GGGB4FFI38E>>>AC? +@HISEQ1:121:C0EP5ACXX:8:2202:11183:23671/2 +TCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGCAGCCTTCAATCAATCTCCAATCACC ++ +JJJIIJJIJJJJJIEHIEGHIIIJJIIGIJIJJJJIHIJFICGIIGGJIJEHIJJ:EHFFFFFEBCEEDDDDDDDDDDDCCDDDDDD +@HISEQ1:121:C0EP5ACXX:8:2203:12602:37061/2 +TTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGN ++ +JJJJJIJJJJIIJHIJJJJJHJIJJDHIJJJJHGIJHIIJJJJIJJJJJHHHHHHFFFFDD<;BDD>C@CEDDCDCCCDDEDDCDDC +@HISEQ1:121:C0EP5ACXX:8:1101:16157:96178/2 +CTGAGATAGGGGGTTGAGTTAGGGCTTCAATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAN ++ +IJJIJIEEHJIJJAGGGHFHIJIIEGGIIJJJHHHHFFFFFDEEECEDDDDDDDCDDDDDDCDDDDD@CDECDBC:ACCCD59BDCC +@HISEQ1:121:C0EP5ACXX:8:1304:1821:110599/2 +GTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCAAGCCTAGGATGGAGCTTTGCTCCTCCCCTCTGTGCTTGTTTTCT ++ +HAC??:4CF>CCDHGGG@HBDHJJDEAGCFBD)?DB0??F*0BFD?BBBHGHCHC7@9(@)))7?37;BDF;9CA3;;A>@AACC:> +@HISEQ1:121:C0EP5ACXX:8:1202:6596:74809/2 +GTCAATGGTCTCTCTCCTCTAAAACGCTCTCTCCTCTCTCTACAGTTTCCTCTCTCTTCTTCTCTGTTCTTGTTCGAATCTCTTCCA ++ +IGAGGHIICHHIIIJIIGDCHIGIGIIGIEHGIIIJJIGGHGGAF7=;@EGIHGGHFF3?B;BDECCCACECCCC;5?CD>@CCDDDDC4@>@C@C +@HISEQ1:121:C0EP5ACXX:8:1205:2077:37536/2 +TCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAA ++ +IIIJIJII>AHIH9C;);(6>AC??8,)534>:>ACBC?< +@HISEQ1:121:C0EP5ACXX:8:1103:4347:43083/2 +GGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTCAATTC ++ +JJJJJJJJJIJJJIJJJJJJJJJIIJJIIJJJJJJJIIGHIJJJIBHHHFFFCCCEDCDCDDDDDDD59BADCDDCCBCABCDCDED +@HISEQ1:121:C0EP5ACXX:8:2107:17275:98920/2 +ATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGN ++ +F?BGBH@HHC@FHHIGIGEFHGGIIDDHGH?DDEDCFIHJIIJIHGGFGBHGIHFFDEEBDDBBDDCC>ACCDDDD<@<>@@CCDC= +@HISEQ1:121:C0EP5ACXX:8:2304:10198:198268/2 +ATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGN ++ +EE?EH@FFHGGBEAF?C?GEBCFHDFHEGEIGGFGGGIHGGHHIJGICFHGIJHFFDEEDDBDDDDCDDDDDDDDD5FHFEGIEHGGEGEHIGGHHHGIDDGHIDFBDDHIGCDD=CGFC@DEE;AEHFCDFFF?AACCCACCDCCDDDA +@HISEQ1:121:C0EP5ACXX:8:1307:5273:167214/2 +GAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGANN ++ +EEHIJJJJJJJJJGIJIJJJJJJJJEHGCFGIDHGGHGHFHEDDEDCEED>>;ACBDDD;1:>:@CACA? +@HISEQ1:121:C0EP5ACXX:8:1203:11801:61902/2 +TCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTAAAGAGACTGTATTCTTCAGCAACAATCAGATCCCCAGATTGATTTGCTCT ++ +<@ACADDEDEECDDDDDD@DDDCDCDDDDD?@BCCCCDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:1108:8809:81311/2 +CCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTAGGTCGCCGAGNNNNNNN ++ +EBF>F?FHIC9CGBHHDDFCBDD?F=FC8B@@=F>FE@BA?>=?@D@DD@CEEACEDDDDDDDDDCDDCCAC>CBDDDBBBDDCDD? +@HISEQ1:121:C0EP5ACXX:8:2204:18606:175884/2 +AGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATACAGTCTCTTTANNNNN ++ +CGG8CDHDHGGHBAG>DBH)==CAAB4ADCFFFCEA@@A@CCCC>CDCBBB@>C@AAC@A<@::::@:A>CCCCCDC>ACDAC@AA5 +@HISEQ1:121:C0EP5ACXX:8:1108:16310:19003/2 +GCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATAC ++ +IIHIJIJJIIGJIGJJIIIJJJJJJJJJJHHHGHHFFEDDDBDDDDDDDDDCDDDDDDDDEDDDBDBDDCECCCCDDCDDCDDDCCC +@HISEQ1:121:C0EP5ACXX:8:2203:6354:184308/2 +GCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATAC ++ +GIIJGIIJJDEEGEH@DEACHH;;?>BCBDDDDCC:A?C9>::C>C@C>:?5?@DDD>>CC3>AACC@CC@CCDC +@HISEQ1:121:C0EP5ACXX:8:1105:17367:119872/2 +TGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGAATA ++ +JJJJJJJIJJJJJIIJJJJJJJJJJJJJJHHHHHHFFFFDDDDDDDDDDDDDDDDDDDDDDEDDDBDDDDDEDDDDDDDDDDDDDD@ +@HISEQ1:121:C0EP5ACXX:8:2202:9681:198266/2 +GCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTAAAGAGACTGTATTCTTCAGCAACA ++ +EDGEGFGDGCGDDHIGEGIHIIIGJBHGEHGIJJJIIIIJIIJHJIJIHHGGHDEF=;8??BCACCCDDCDDCDEEEDE4>CCD9<8 +@HISEQ1:121:C0EP5ACXX:8:1102:2897:190263/2 +TAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCT ++ +@>A38>@>C88&(>@@3@>>3>@@C(4@C>:CCDCCCDDC +@HISEQ1:121:C0EP5ACXX:8:1205:11903:194100/2 +CTAACTCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTAAAGAGACTGTATTCTTCAGCAACAATCAGATCCCCAGATTGATTT ++ +IIJFJJJIJIIJJIGIIJJGII@GGIJFHIJEHIGIA6ADFCEAEEC?CCAADDFFEEDC@A>CB?DACCA@CDDDD +@HISEQ1:121:C0EP5ACXX:8:1202:13626:25638/2 +GTTTCATTTTGTGGTGGAACACATAAT ++ ++C+A,3IFC,,33:CCDDDDDC::>A@ACDDCCCCCC +@HISEQ1:121:C0EP5ACXX:8:1306:20726:15789/2 +GAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAATCA ++ +BHDE6BG>)?A?BDF4FHBF/8@@@6E:9.7.6>@@>;;-5A +@HISEQ1:121:C0EP5ACXX:8:2107:15019:37435/2 +GAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAGAAGCTCGAATTGAAGCCCTAACTCAACCCCC ++ +JJJJIEIIIIGEHDHIIIIJJIJIHIIIJJJJJIJJHIHIJJJIGIFFCHIJIIJIHFAHHFFEEEDC@CDCDDDCDBCCDDDBBB@ +@HISEQ1:121:C0EP5ACXX:8:2208:13905:97948/2 +CCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCCATCAGAGCAAAT ++ +GH>EGEHGJJIGIJIGD-:BB@CDEDDD@CCDDCCDBDDDABCDCDBD@@B@BBDDDB>CCCCDDDDDDBCD>5@DDDC<@39>CAC +@HISEQ1:121:C0EP5ACXX:8:1301:2094:147266/2 +TGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCC ++ +FJIIJIJIIIIGIJJJIJIHJIIJIJJHBFHGGJGGF=CGIIGGIHHFGHFFFEFFFEDEEDCDCDCCBBBBD7ACDDDDAC@C>C? +@HISEQ1:121:C0EP5ACXX:8:1306:10553:20592/2 +CATACGGGATTCTTCAGCAACAATCAGATCCCCAGATTGATTTGCTCTGATGGCCGCTCTTGAAGGAGTTTCGTTCCTCGCCTCTGT ++ ++<+AF++)CDDBDDDDDBDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:1203:5698:36196/2 +GGGGTTGTGGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGCC ++ +G1@93&0)(<38388CC?A<7CCC>>:A@05@0(8<>>B?095<918))+05(+(>:A>C4>(39<@D +@HISEQ1:121:C0EP5ACXX:8:1107:20608:196329/2 +TGGGTTGTGGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGAAACTCCTTCAAGAGCGGC ++ +FHHI::ECGGDFEHGIIJBHGFGHGIJFB7@DBCCCCDCCDDDDDCDB9> +@HISEQ1:121:C0EP5ACXX:8:1307:1725:60131/2 +TTACCCATCAACACTTAACCCTTACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCC ++ +IJJJJEFHIJJJIJIJJGJIIJJIJJJJIIJHJJIJIJIJJIJJJIJJJGIJJJJJGHIHGHHFDEFFFDECCCDDBBDDDCDDBDC +@HISEQ1:121:C0EP5ACXX:8:2201:17989:121640/2 +GGACCACTTTGACTGTGTAAGCAAAAGAGCATACAAACCTTGGGTTGTGGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGC ++ +AAACG=EEGH@AEHBCGHGIIIHGHGHGGGGIJJJJGIIJJGCCFGHIJIHIEFHHHFFFFDCDDDDDD5>BDDDCDDDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:2103:17026:82629/2 +ATTGAAACAAGAGCCACACCAGGAAAGAGCCTTGATCAAATAAATCAAACCGATCTAACCTTGGGTTGTGGTTCCAGCAACGAAGGN ++ +GIIGIIJEHJGIGIJIJIIIIJIEHIEG@B@FGGGIDHGIGJGEDEHI;8BHHAB???@ACEC?B1;=B@8<<@A@CDCCADDD?>5 +@HISEQ1:121:C0EP5ACXX:8:1104:7384:82234/2 +TCGGCGACCTAAAGAGACTGTATTCTTCAGCAACAATCAGATCCCCAGATTGATTTGCTCTGATGGCCGCTCTTGAAGGAGTTTCGT ++ +JIJIIIJJIJJJJIIIIIIJHIIJJJJJJIIIIIIJJHHHHHEHFFFDDCEEEEDCDCDDDDDCCDDDDDDDBCCCCDDEDAGHH?EEFDDEBAEDDCDD@CD@:>;AC>> +@HISEQ1:121:C0EP5ACXX:8:1203:15133:98209/2 +GGCATAGGGTTATAGAAAATAGTAAACAAACTATAGAATTGAAACAAGAGCCACACCAGGAAAGAGCCTTGATCAAATAAAT ++ +A<)AG3CH3+<1C@4:?D??@DCDGF>GBFFBD@FIGDHHJGJJIGHGIJEDEHIHHHFFDBEEEDABDDDACCECCCCCDD +@HISEQ1:121:C0EP5ACXX:8:2201:15934:79822/2 +TTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGGGCTCCTCTGCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGN ++ +IJJJGHIIIIJJJHHIJJJJIJJJJEIJJJIJIJHGFFHJJGFJJJJJJHHHHHHFFFFDDCBBDC@C>ACCB@A:?CCCDDDCCDC +@HISEQ1:121:C0EP5ACXX:8:2103:11160:152496/2 +GTTTCGTTCCTCGCCTCTGTTTTCGCAAGGAGTTATGGACAACCCCCCTTCGTTGCTGGAACCACAACCCAAGGTTAGATCGGTTTN ++ +GGGHGIGIGHGIBFHHIIIGEHJJIJII8HGB@FHHFHIIJIIGGHFDBBDDCDDDCCCBCCBDBDDBBDBDCCDD8>@B +@HISEQ1:121:C0EP5ACXX:8:2205:18696:101935/2 +GACAATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTATAGAATTGAAACAANN ++ +GGIEGHIHJ4??EGEHHCFFHGGG>G3?FGHIGIECDFGHIJJIECH)6@?EEEEHC7;;?>BCEDAEBCDDADDCDA:@@5:?BCC +@HISEQ1:121:C0EP5ACXX:8:1205:12485:13377/2 +ATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTATAGAATTGAAACAAN ++ +12+1*@E:C*CF<100??9:*B?FHCDE@D?C>@CCAC:;A=@C>(;@>@C>CDD> +@HISEQ1:121:C0EP5ACXX:8:2105:10921:73090/2 +GAGCGACAATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTATAGAATTGAAAC ++ +DHEGBCFDHH@GIED?CDDFGHGBGGIIFHGIGGIHHIIJIIGGHFHGIIG@CEHHHFFFFFFECDEEEEDDDDDDDECDDDDDDD@ +@HISEQ1:121:C0EP5ACXX:8:1301:9478:45031/2 +GCTCCCTGCGAATGGTGATTGGAGATTGATTGAAGGCTGCTCTCACCGGAATCTCTTCACTTGCCTCTTATTTGGAGTCTACTGCAN ++ +H@EBHEHEAGIEAD9?HBD4?BBF;?BGGFG>D>BB=C@AHGGF:CH@<48(?@?C@>3@CC@>>;>;>3@(;;>><:((::AC@:9 +@HISEQ1:121:C0EP5ACXX:8:2104:6749:159109/2 +AAACCATGAGCGACAATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTATAGAA ++ +HGEG@FFH>BA@@?@FHGGG*B?BGGHIBBDHGIIBFHHACHECGHEHGGGBEHEEA@CDBEDCEDDE@CA5>C>C@AABDDCDDD@ +@HISEQ1:121:C0EP5ACXX:8:2202:21245:113808/2 +NACTTTACAATTATTGCCTCTCTTTCGATTTTTGCTCCCAGGTTCTCAGATCGGTGCTTGGTTCCCTCCTGGGCTCCTCTGCTCCCT ++ +#2>CGIGJIIEIGJJJGIJJJIJJIGEGGIJJJIGIGHGIIJJGI@=CEGIJBGEHHFFFD3=CECC@?=3;=BC +@HISEQ1:121:C0EP5ACXX:8:2302:1358:92768/2 +ACGCAACACCATATTTCCGGATCCAATCAATCTCAAACCATGAGCGACAATAGGTGTTAAGGTTATCAGATCCAATTGATGCAGGCA ++ +EEHDHGIGIJIJJEGIIGEGEDGHGGGCHHI@GIJIGDGE>EEHIFHDB>CEE>5>CDDECD:>CCCDECDACCCCCACDDDCCBDB +@HISEQ1:121:C0EP5ACXX:8:2302:13383:122517/2 +TCAACCCCCTATCTCAGATCCGATGCTCGGCGACCTAAAGAGACTGTATTCTTCAGCAACAATCAGATCCCCAGATTGATTTGCTCT ++ +CAEGIEEFFHBFGHIJJGGIIFDBHEGHCFGIGHGHFFFFFE@ACE@CCDDEECDCDDDDDDDDDDDDDDDDDDDCDCDEDECDDDC +@HISEQ1:121:C0EP5ACXX:8:1305:19207:34291/2 +AAAGATCGAAGGAGATGGTAATAAAGTCTAGAAATGAAATACTCATAACCTAAGGAAAATACTTTATCAAAGTCATAATTAAGACTA ++ +GIGECB?ED>F>GD??FG::CC>GGGIHGGHGEHGCFGEFGHGIEICCHHEHIGJIGJGDEH;=7?>CDECB;@>DDCEEEEDC;@@ +@HISEQ1:121:C0EP5ACXX:8:2102:10551:119670/2 +TAGATCGGTTTGATTTATTTGATCAAGGCTCTTTCCTGGTGTGGCTCTTGTTTCAATTCTATAGTTTGTTTACTATTTTCTATAACC ++ +IJJIJIJJIJJIIJJJJJJJIIIIJJJJJJJJJJJJHIJFHHIJJJJIJIHHHGEHHHFFDFDFEFEDEEECDDEFEEEDDDECCA@ +@HISEQ1:121:C0EP5ACXX:8:1208:7778:129322/2 +TACAACGAAAACAAGGAATGAGATTACTTATAATATACTCGGTAAGACTGAAAGCAACACCTTATTTCCGGATCCAATCAATCTCAA ++ +FHAIHHIHHCCHCGGIJIIGH)7@EHHCD?);BC>CEDDDDDDDD:>CCCA>CCCD +@HISEQ1:121:C0EP5ACXX:8:2304:6605:62458/2 +CTAAGAATTTATTAATATTGCACCCAGGCATTGCATTTCTCTTGGGGAGGAAGATAATATAGCACAATCATATTGTTGACACCTTNN ++ +HGBBEGEHGGFJGEIJIJAHC@DBEHIGDHDGI4BA??GICCD:=@>>A?AC>: +@HISEQ1:121:C0EP5ACXX:8:2106:13776:157073/2 +ACCTATTGTCGCTCATGGTTTGAGATTGATTGGATCCGGAAATATGGTGTTGCGTTCAGTCTTACCGAGTATATTATAAGTAATCTC ++ +JJJJJJJJHIJJJJJJJJCGHIFHGIIIIIJJJIJIGIJHIJJIHJJ@EGGHHHFFFEEEEEEEDDDDD?DB<*?DFEDGGIFG@AEHIHFEEHFFFEBECEEDCCECDCDD@C@@<9@CCC +@HISEQ1:121:C0EP5ACXX:8:1207:17351:77865/2 +TGCACAGTCTCAACTGGAAAGGATCAATTCTAACTAGATTAGAATAAGCCAGGGAAACATAACTAATCTTACAACGAAAACAAGGAA ++ +IJJJJJIJHIIJJJFIJGJJJIJIJJJIIGIJJJJJHIJJJJJJJJJIJJJJJJJJJIHHHHHHFFFFFFEEEEEDBDDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:1204:17042:185305/2 +TAACACCTATTGTCGCTCATGGTTTGAGATTGATTGGATCCGGAAATATGGTGTTGCGTTCAGTCTTACCGAGTATATTATAAGTAA ++ +I<+AB@C +@HISEQ1:121:C0EP5ACXX:8:2103:20915:142998/2 +GATCCTTTCCAGTTGAGACTGTGCATGTTGGATCTCAAGATTAGATGTATTATTGGAATCAATTTTGTTGCTGCTCTGCAG ++ +GDIGIGEGGJGEJEGIICFCHCFHIEEGEC?CHCDDECCCAC +@HISEQ1:121:C0EP5ACXX:8:2108:15621:6710/2 +AGTCTAGAAATGAAATACTCATAACCTAAGGAAAATACTTTATCAAAGTCATAATTAAGACTATGCACTCTATGAATATCACTGAAN ++ +GJ4CIH<4FGFIHGGHICGHIIIEGGGIIGEHHIIEIGE@?CCHDHBCCCCDCCCCCCD;5;> +@HISEQ1:121:C0EP5ACXX:8:1207:17701:88729/2 +ATTCCTCTGGGAGAAAATGAAATCTCACCCAAAGATCAAGTTGGGAAATAGACTCATGGCTAGGATCGAAACCCGAGTGCCATTGCT ++ +AFBHGIHCGEIGFHJ?EGGHHGGIJIHIIIJIIJJIHHGGIGHIII>@GEHIIGIEEEFCHHDDEDD65>?8,5;?88C>:> +@HISEQ1:121:C0EP5ACXX:8:2104:7678:122935/2 +CCATTTTGAGAAATGTTCCCACAGAATTTTCCTCTATGATAGCGGTTAAAGCCTCAGCATTAGCAAATTCCTCTGGGAGAAAATGAA ++ +FHAAFCG:C@=7=C>AHC>.7?7;;@C@6>;3@?BBBB>9C(:A +@HISEQ1:121:C0EP5ACXX:8:2205:8175:94899/2 +ACAACTTTTTTGCCAACATTACAAGACACATCAGTGTTAATACAGAATCTTGTAAACATGTTCATCCTATTTTTATTGTGAGTT ++ +B>??;?BG<4B@B;DGDHIGIIGGB@BFGBFG>FHGGDGGDC@;?>AEHDFB)7@@@C>@CC;C;CCACD +@HISEQ1:121:C0EP5ACXX:8:1303:8608:152316/2 +CCAAAAGTGACCAAATCAGGTAACAAAACCTTTGATCCCAAAGCTCTCTTTAATAAACTTGCTCTTGCTAGAACCCAAGCAAAAAAA ++ +JJJJJJJHHHIJGIJJJJJJHIIJJJIJHJJJJJJJIJIJJJJJJIIJIJJJJJJGIJHHHHHHFFFFFFDEEEDDDDDDDDDDDDD +@HISEQ1:121:C0EP5ACXX:8:2303:19934:33517/2 +ATCTCACACCACCTTGTGGTAGCACAAAAAGTTCCAAACCAAAAGTGACCAAATCAGGTACCAAAACTTTTGATCCCAAAGCTCTCT ++ +IJIJJJJJJIIIIJJJHEG;FDGHJFIJJJD?CBCCEDECCDCC;(;A?CCAB@?@BDB?? +@HISEQ1:121:C0EP5ACXX:8:2306:12186:45722/2 +TTGATCTGTCTGAGGCTGTGTCCTGTCTAAAGGGTGTAAGTGTGAATTGCTATACTAAGTTGCTGAATTATCAACTAGGTGGTTTT ++ +JJJIJJJJHIIIGIJJJJHIGJJJJIJJJGIJJJBFHHIJIHHIJJJJIJJJJJJJIIJIGIJIIHHHHHHHFFFFFFE@CD?@@B diff -r 000000000000 -r 05c27700e5ca demo_files/son_male.bam Binary file demo_files/son_male.bam has changed diff -r 000000000000 -r 05c27700e5ca demo_files/son_male.bam.bai Binary file demo_files/son_male.bam.bai has changed diff -r 000000000000 -r 05c27700e5ca references/.gitignore diff -r 000000000000 -r 05c27700e5ca references/reference.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/references/reference.fasta Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,19 @@ +>comp0_c0_seq1 +ACAGAATAATCACAAGGCTTGAGCAAAGGTAGAGGAATCTATCTAACACACTCTCCTGCA +GAGCAGCAACAAAATTGATTCCAATAATACATCTAATCTTGAGATCCAACATGCACAGTC +TCAACTGGAAAGGATCAATTCTAACTAGATTAGAATAAGCCAGGGAAACATAACTAATCT +TACAACGAAAACAAGGAATGAGATTACTTATAATATACTCGGTAAGACTGAACGCAACAC +CATATTTCCGGATCCAATCAATCTCAAACCATGAGCGACAATAGGTGTTAAGGTTATCAG +ATCCAATTGATGCAGGCATAGGGTTATAGAAAATAGTAAACAAACTATAGAATTGAAACA +AGAGCCACACCAGGAAAGAGCCTTGATCAAATAAATCAAACCGATCTAACCTTGGGTTGT +GGTTCCAGCAACGAAGGGGGGTTGTCCATAACTCCTTGCGAAAACAGAGGCGAGGAACGA +AACTCCTTCAAGAGCGGCCATCAGAGCAAATCAATCTGGGGATCTGATTGTTGCTGAAGA +ATACAGTCTCTTTAGGTCGCCGAGCATCGGATCTGAGATAGGGGGTTGAGTTAGGGCTTC +AATTCGAGCTTCTGCAGTAGACTCCAAATAAGAGGCAAGTGAAGAGATTCCGGTGAGAGC +AGCCTTCAATCAATCTCCAATCACCATTCGCAGGGAGCAGAGGAGCCCAGGAGGGAACCA +AGCACCGATCTGAGAACCTGGGAGCAAAAATCGAAAGAGAGGCAATAATTGTAAAGTAAG +GGTTAAGTGTTGATGGGTAAAGTTTTGGGTATACGGGGCGAATCCCCACAATTTGCAAGG +GCAAATTATGTGTTCCACCACAAAATGAAACAAGAAAGGAAAGAAAACAAGCACAGAGGG +GAGGAGCAAAGCTCCATCCTAGGCTTGGAAGAGATTCGAACAAGAACAGAGAAGAAGAGA +GAGGAAACTGTAGAGAGAGGAGAGAGCGTTTTAGAGGAGAGAGGGAAACAGCCCGGATCA +CCAGCTAAGGCCCCT diff -r 000000000000 -r 05c27700e5ca references/reference_contig_names --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/references/reference_contig_names Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,1 @@ +comp0_c0_seq1 diff -r 000000000000 -r 05c27700e5ca reformat_trinity_header.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reformat_trinity_header.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,9 @@ +#!/bin/bash + +results=$1 #reformatted fasta sequence written here +trinity_fasta=${2} + +perl -pe 's/(>[\S]+).+/$1/' $trinity_fasta >$results +samtools faidx $results + + diff -r 000000000000 -r 05c27700e5ca reformat_trinity_header.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reformat_trinity_header.xml Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,21 @@ + + Reformat Trinity header + reformat_trinity_header.sh $output $input1 + + + + + + + + + + + + + + + Reformat Trinity header, keep only part until first space. + + + \ No newline at end of file diff -r 000000000000 -r 05c27700e5ca runLinkYX.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runLinkYX.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,205 @@ +#!/bin/bash +set -e; mkdir -p vcf; mkdir -p bam; mkdir -p references; mkdir -p scripts; + +email_address_of_user=$1; +name_of_user_computer=$2; + +#read config variables +echo "Reading config...." >&2 +#echo `ls -l` +computer_name=`hostname`; +if [ $computer_name == $name_of_user_computer ]; then + #local_computer + source config_devel; +else + #metacentrum machine + source config_meta; +fi + +#initally we believe that all files are present +ok=true; + +#we get to know if files are provided and if they are in .fasta or .fastq format +#first, rename files to shorter versions (fastq->fq, fasta->fa) +rename 's/fasta$/fa/' input/*.fasta 2>/dev/null +rename 's/fastq$/fq/' input/*.fastq 2>/dev/null + +check_if_exists () +{ +for ARG in "$@"; + do + if [[ -e "input/${ARG}_1.fq" ]]; then + eval ${ARG}_ext=fq + elif [[ -e "input/${ARG}_1.fa" ]]; then + eval ${ARG}_ext=fa + else + ok=false; + fi + done; +} + +check_if_paired_end () +{ +for ARG in "$@"; + do + extension=$(eval "echo \$${ARG}_ext"); #echo $extension; + + if [[ (-e "input/${ARG}_1.${extension}") && (-e "input/${ARG}_2.${extension}") ]]; then + eval ${ARG}_paired=paired; + else + eval ${ARG}_paired=single; + fi + done; +} + +#check if file with reads exist +check_if_exists mother father daughter son; +#and determine whether they are single or paired-end reads +check_if_paired_end mother father daughter son; + +if [ $ok == true ]; then + echo "mother reads names:" $mother_ext $mother_paired; + echo "father reads names:" $father_ext $father_paired; + echo "daughter reads names:" $daughter_ext $daughter_paired; + echo "son reads names:" $son_ext $son_paired; + +if [[ $father_ext =~ (fq) ]] && [[ $son_ext =~ (fq) ]]; then + #no conversion needed, both fastq files + male_ext=fq; +else + #convert to fasta (we need to merge father and son reads in order to build male reference contigs) + #father OR son is fasta + echo "converting.."; + male_ext=fa; + + if [[ father_1.$father_ext =~ (fq) ]]; then + #father is fastq and must be converted to fasta + fastq_to_fasta -n -Q33 -i input/father_1.$father_ext -o input/father_1.$male_ext; + fastq_to_fasta -n -Q33 -i input/father_2.$father_ext -o input/father_2.$male_ext; + father_ext=fa; + + else + #son is fastq and must be converted to fasta + fastq_to_fasta -n -Q33 -i input/son_1.$father_ext -o input/son_1.$male_ext; + fastq_to_fasta -n -Q33 -i input/son_2.$father_ext -o input/son_2.$male_ext; + son_ext=fa; + fi +fi + #merging of father and son files + echo "concatenating.."; + cat input/father_1.$father_ext input/son_1.$son_ext >input/father_and_sons_1.$male_ext; + + if [[ $father_paired =~ (paired) ]] && [[ $son_paired =~ (paired) ]]; then + cat input/father_2.$father_ext input/son_2.$son_ext >input/father_and_sons_2.$male_ext; + fi + + + #NOW run Trinity to assemble mother contigs + #in: mother reads out: reference.fasta + PBS_NUM_PPN_used=$(($PBS_NUM_PPN_used - 2)); + echo "processors used:" $PBS_NUM_PPN_used; + +#<$trinity_stdout 2>&1 + echo "$trinity --CPU $PBS_NUM_PPN_used --seqType $mother_ext --JM 20G --left input/mother_1.$mother_ext --right input/mother_2.$mother_ext --output trinity_out_dir_mother 1>$trinity_stdout 2>&1"; + else + $trinity --CPU $PBS_NUM_PPN_used --seqType $mother_ext --JM 20G --single input/mother_1.$mother_ext --output trinity_out_dir_mother 1>$trinity_stdout 2>&1 + echo "$trinity --CPU $PBS_NUM_PPN_used --seqType $mother_ext --JM 20G --single input/mother_1.$mother_ext --output trinity_out_dir_mother 1>$trinity_stdout 2>&1"; + fi + + #retrieve assembled contigs and name them as reference.fasta + mv trinity_out_dir_mother/Trinity.fasta reference_pro.fasta + perl -pe 's/(>[\S]+).+/$1/' reference_pro.fasta >references/reference.fasta; rm reference_pro.fasta; +#PREVENT_TRINITY_MOTHER + + grep ">" references/reference.fasta | sed 's/>//g' >references/reference_contig_names + + #now call to_get_vcf_files.sh to map reads to reference contigs + ./scripts/to_get_vcf_files.sh references/reference.fasta mother_1.$mother_ext mother_2.$mother_ext mother $mother_paired + echo "Mother mapping successful."; + ./scripts/to_get_vcf_files.sh references/reference.fasta father_1.$mother_ext father_2.$mother_ext father $father_paired + echo "Father mapping successful."; + ./scripts/to_get_vcf_files.sh references/reference.fasta daughter_1.$mother_ext daughter_2.$mother_ext daughter $daughter_paired + echo "Daughter mapping successful."; + ./scripts/to_get_vcf_files.sh references/reference.fasta son_1.$mother_ext son_2.$mother_ext son $son_paired + echo "Son mapping successful."; + + wait; + + #NOW run Trinity to assemble male contigs + #in: male reads out: reference_male.fasta +#<$trinity_stdout 2>&1 + echo "$trinity --CPU $PBS_NUM_PPN_used --seqType $male_ext --JM 20G --left input/father_and_sons_1.$male_ext --right input/father_and_sons_2.$male_ext --output trinity_out_dir_male 1>$trinity_stdout 2>&1"; + else + $trinity --CPU $PBS_NUM_PPN_used --seqType $male_ext --JM 20G --single input/father_and_sons_1.$male_ext --output trinity_out_dir_male 1>$trinity_stdout 2>&1 + echo "$trinity --CPU $PBS_NUM_PPN_used --seqType $male_ext --JM 20G --single input/father_and_sons_1.$male_ext --output trinity_out_dir_male 1>$trinity_stdout 2>&1"; + fi + + #retrieve assembled contigs and name them as reference_male.fasta + mv trinity_out_dir_male/Trinity.fasta reference_male_pro.fasta + perl -pe 's/(>[\S]+).+/$1/' reference_male_pro.fasta >references/reference_male.fasta; rm reference_male_pro.fasta; +#PREVENT_TRINITY_MALES + + grep ">" references/reference_male.fasta | sed 's/>//g' >references/male_contig_names + + #now call to_get_vcf_files.sh to map reads to reference contigs + ./scripts/to_get_Y_variants.sh references/reference_male.fasta mother_1.$mother_ext mother_2.$mother_ext mother $mother_paired + echo "Mother mapping to males successful."; + ./scripts/to_get_Y_variants.sh references/reference_male.fasta father_1.$mother_ext father_2.$mother_ext father $father_paired + echo "Father mapping to males successful."; + ./scripts/to_get_Y_variants.sh references/reference_male.fasta daughter_1.$mother_ext daughter_2.$mother_ext daughter $daughter_paired + echo "Daughter mapping to males successful."; + ./scripts/to_get_Y_variants.sh references/reference_male.fasta son_1.$mother_ext son_2.$mother_ext son $son_paired + echo "Son mapping to males successful."; + + #index bam files + + index_bam_file () + { + for ARG in "$@"; + do + if [ -e "bam/aln_cleaned_sorted_deduplicated_${ARG}.bam.bai" ]; + then + echo "Index already exists. Not being created again."; + else + samtools index bam/aln_cleaned_sorted_deduplicated_${ARG}.bam & + fi + done; + } + + #index bam files + index_bam_file mother father daughter son mother_male father_male daughter_male son_male; + wait; + echo "Indexes successfully created." + + echo -e "Starting analysis"; + + #A variant X1X1 X2Y + dir="A/"; + bash -x ./A.sh $email_address_of_user; + perl scripts/sorting.pl A/; + + #Y variant + dir="Y/"; + bash -x ./Y.sh $email_address_of_user; + + wait; + + #sending results (not BAM files) + mutt -s "LINKYX: Results of computation for Y-linked genes" $email_address_of_user -a Y_results_sequences.txt < messages_to_user/message_results_sentY; + mutt -s "LINKYX: Results of computation for X-linked genes" $email_address_of_user -a X_results_sequences.txt < messages_to_user/message_results_sentX; + + +echo -e "Done." +else + echo "not all input files are present in proper form"; + mutt -s "LINKYX: Not all input files are present in proper form." $email_address_of_user < messages_to_user/message_input_files_error +fi + + + + diff -r 000000000000 -r 05c27700e5ca runLinkYX_galaxy.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runLinkYX_galaxy.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,205 @@ +#!/bin/bash +set -e; mkdir -p vcf; mkdir -p bam; mkdir -p references; mkdir -p scripts; + +email_address_of_user=$1; +name_of_user_computer=$2; + +#read config variables +echo "Reading config...." >&2 +#echo `ls -l` +computer_name=`hostname`; +if [ $computer_name == $name_of_user_computer ]; then + #local_computer + source config_devel; +else + #metacentrum machine + source config_meta; +fi + +#initally we believe that all files are present +ok=true; + +#we get to know if files are provided and if they are in .fasta or .fastq format +#first, rename files to shorter versions (fastq->fq, fasta->fa) +rename 's/fasta$/fa/' input/*.fasta 2>/dev/null +rename 's/fastq$/fq/' input/*.fastq 2>/dev/null + +check_if_exists () +{ +for ARG in "$@"; + do + if [[ -e "input/${ARG}_1.fq" ]]; then + eval ${ARG}_ext=fq + elif [[ -e "input/${ARG}_1.fa" ]]; then + eval ${ARG}_ext=fa + else + ok=false; + fi + done; +} + +check_if_paired_end () +{ +for ARG in "$@"; + do + extension=$(eval "echo \$${ARG}_ext"); #echo $extension; + + if [[ (-e "input/${ARG}_1.${extension}") && (-e "input/${ARG}_2.${extension}") ]]; then + eval ${ARG}_paired=paired; + else + eval ${ARG}_paired=single; + fi + done; +} + +#check if file with reads exist +check_if_exists mother father daughter son; +#and determine whether they are single or paired-end reads +check_if_paired_end mother father daughter son; + +if [ $ok == true ]; then + echo "mother reads names:" $mother_ext $mother_paired; + echo "father reads names:" $father_ext $father_paired; + echo "daughter reads names:" $daughter_ext $daughter_paired; + echo "son reads names:" $son_ext $son_paired; + +if [[ $father_ext =~ (fq) ]] && [[ $son_ext =~ (fq) ]]; then + #no conversion needed, both fastq files + male_ext=fq; +else + #convert to fasta (we need to merge father and son reads in order to build male reference contigs) + #father OR son is fasta + echo "converting.."; + male_ext=fa; + + if [[ father_1.$father_ext =~ (fq) ]]; then + #father is fastq and must be converted to fasta + fastq_to_fasta -n -Q33 -i input/father_1.$father_ext -o input/father_1.$male_ext; + fastq_to_fasta -n -Q33 -i input/father_2.$father_ext -o input/father_2.$male_ext; + father_ext=fa; + + else + #son is fastq and must be converted to fasta + fastq_to_fasta -n -Q33 -i input/son_1.$father_ext -o input/son_1.$male_ext; + fastq_to_fasta -n -Q33 -i input/son_2.$father_ext -o input/son_2.$male_ext; + son_ext=fa; + fi +fi + #merging of father and son files + echo "concatenating.."; + cat input/father_1.$father_ext input/son_1.$son_ext >input/father_and_sons_1.$male_ext; + + if [[ $father_paired =~ (paired) ]] && [[ $son_paired =~ (paired) ]]; then + cat input/father_2.$father_ext input/son_2.$son_ext >input/father_and_sons_2.$male_ext; + fi + + + #NOW run Trinity to assemble mother contigs + #in: mother reads out: reference.fasta + PBS_NUM_PPN_used=$(($PBS_NUM_PPN_used - 2)); + echo "processors used:" $PBS_NUM_PPN_used; + +#<$trinity_stdout 2>&1 + echo "$trinity --CPU $PBS_NUM_PPN_used --seqType $mother_ext --JM 20G --left input/mother_1.$mother_ext --right input/mother_2.$mother_ext --output trinity_out_dir_mother 1>$trinity_stdout 2>&1"; + else + $trinity --CPU $PBS_NUM_PPN_used --seqType $mother_ext --JM 20G --single input/mother_1.$mother_ext --output trinity_out_dir_mother 1>$trinity_stdout 2>&1 + echo "$trinity --CPU $PBS_NUM_PPN_used --seqType $mother_ext --JM 20G --single input/mother_1.$mother_ext --output trinity_out_dir_mother 1>$trinity_stdout 2>&1"; + fi + + #retrieve assembled contigs and name them as reference.fasta + mv trinity_out_dir_mother/Trinity.fasta reference_pro.fasta + perl -pe 's/(>[\S]+).+/$1/' reference_pro.fasta >references/reference.fasta; rm reference_pro.fasta; +#PREVENT_TRINITY_MOTHER + + grep ">" references/reference.fasta | sed 's/>//g' >references/reference_contig_names + + #now call to_get_vcf_files.sh to map reads to reference contigs + ./scripts/to_get_vcf_files.sh references/reference.fasta mother_1.$mother_ext mother_2.$mother_ext mother $mother_paired + echo "Mother mapping successful."; + ./scripts/to_get_vcf_files.sh references/reference.fasta father_1.$mother_ext father_2.$mother_ext father $father_paired + echo "Father mapping successful."; + ./scripts/to_get_vcf_files.sh references/reference.fasta daughter_1.$mother_ext daughter_2.$mother_ext daughter $daughter_paired + echo "Daughter mapping successful."; + ./scripts/to_get_vcf_files.sh references/reference.fasta son_1.$mother_ext son_2.$mother_ext son $son_paired + echo "Son mapping successful."; + + wait; + + #NOW run Trinity to assemble male contigs + #in: male reads out: reference_male.fasta +#<$trinity_stdout 2>&1 + echo "$trinity --CPU $PBS_NUM_PPN_used --seqType $male_ext --JM 20G --left input/father_and_sons_1.$male_ext --right input/father_and_sons_2.$male_ext --output trinity_out_dir_male 1>$trinity_stdout 2>&1"; + else + $trinity --CPU $PBS_NUM_PPN_used --seqType $male_ext --JM 20G --single input/father_and_sons_1.$male_ext --output trinity_out_dir_male 1>$trinity_stdout 2>&1 + echo "$trinity --CPU $PBS_NUM_PPN_used --seqType $male_ext --JM 20G --single input/father_and_sons_1.$male_ext --output trinity_out_dir_male 1>$trinity_stdout 2>&1"; + fi + + #retrieve assembled contigs and name them as reference_male.fasta + mv trinity_out_dir_male/Trinity.fasta reference_male_pro.fasta + perl -pe 's/(>[\S]+).+/$1/' reference_male_pro.fasta >references/reference_male.fasta; rm reference_male_pro.fasta; +#PREVENT_TRINITY_MALES + + grep ">" references/reference_male.fasta | sed 's/>//g' >references/male_contig_names + + #now call to_get_vcf_files.sh to map reads to reference contigs + ./scripts/to_get_Y_variants.sh references/reference_male.fasta mother_1.$mother_ext mother_2.$mother_ext mother $mother_paired + echo "Mother mapping to males successful."; + ./scripts/to_get_Y_variants.sh references/reference_male.fasta father_1.$mother_ext father_2.$mother_ext father $father_paired + echo "Father mapping to males successful."; + ./scripts/to_get_Y_variants.sh references/reference_male.fasta daughter_1.$mother_ext daughter_2.$mother_ext daughter $daughter_paired + echo "Daughter mapping to males successful."; + ./scripts/to_get_Y_variants.sh references/reference_male.fasta son_1.$mother_ext son_2.$mother_ext son $son_paired + echo "Son mapping to males successful."; + + #index bam files + + index_bam_file () + { + for ARG in "$@"; + do + if [ -e "bam/aln_cleaned_sorted_deduplicated_${ARG}.bam.bai" ]; + then + echo "Index already exists. Not being created again."; + else + samtools index bam/aln_cleaned_sorted_deduplicated_${ARG}.bam & + fi + done; + } + + #index bam files + index_bam_file mother father daughter son mother_male father_male daughter_male son_male; + wait; + echo "Indexes successfully created." + + echo -e "Starting analysis"; + + #A variant X1X1 X2Y + dir="A/"; + bash -x ./A.sh $email_address_of_user; + perl scripts/sorting.pl A/; + + #Y variant + dir="Y/"; + bash -x ./Y.sh $email_address_of_user; + + wait; + + #sending results (not BAM files) + mutt -s "LINKYX: Results of computation for Y-linked genes" $email_address_of_user -a Y_results_sequences.txt < messages_to_user/message_results_sentY; + mutt -s "LINKYX: Results of computation for X-linked genes" $email_address_of_user -a X_results_sequences.txt < messages_to_user/message_results_sentX; + + +echo -e "Done." +else + echo "not all input files are present in proper form"; + mutt -s "LINKYX: Not all input files are present in proper form." $email_address_of_user < messages_to_user/message_input_files_error +fi + + + + diff -r 000000000000 -r 05c27700e5ca run_snp_analysis.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_snp_analysis.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,37 @@ +#!/bin/bash + +shopt -s extglob; +#turns on extended globbing features ('!' can then be used to exclude file names) + +#entering SCRATCHDIR used for computation on Metacentrum nodes +cd $SCRATCHDIR; + +#copying input files +cp -r /storage/brno2/home/nicki/linkyx/* . + +#logfile +echo "Copying of the input data finished." `date` >/storage/brno2/home/nicki/linkyx/log; + +#adding needed modules +module add trinity; +module add bwa-0.6.2; +module add bowtie-0.12.8; +module add ics.muni.cz jdk-1.6.0; #initialization of the specific JAVA version +module add samtools-0.1.18alt #samtools recompiled with -fPIC parameter +module add picard-1.80; +module add fastx-0.0.13; + +#export of perl modules +export PERL5LIB=/storage/brno2/home/nicki/modules/File-Slurp-9999.19/lib:/storage/brno2/home/nicki/modules/Bio-SamTools-1.37/lib:/storage/brno2/home/nicki/modules/BioPerl-1.6.901:/storage/brno2/home/nicki/modules/Data-Dumper-2.139:/storage/brno2/home/nicki/modules/libwww-perl-6.04/lib:/storage/brno2/home/nicki/modules/URI-1.60:/storage/brno2/home/nicki/modules/UUID-Generator-PurePerl-0.04_02/lib:/storage/brno2/home/nicki/modules/UUID-Object-0.81:/storage/brno2/home/nicki/modules/UUID-Generator-PurePerl-0.04_02/lib/UUID/:Generator:/storage/brno2/home/nicki/modules/UUID-Object-0.81/lib:/home/nicki/lib:/storage/brno2/home/nicki/modules/bio_samtools_bin/local/lib/perl/5.10.0:/home/nicki/lib/x86_64-linux-gnu-thread-multi:/home/nicki/lib/man:/storage/brno2/home/nicki/modules/Data-GUID-0.046/lib:/home/nicki/perl/lib/perl5:/home/nicki/perl/lib/perl:/home/nicki/perl/share/perl:/home/nicki/perl/share/perl5:/home/nicki/lib/lib/perl5:/home/nicki/lib/lib/perl:/home/nicki/lib/share/perl:/home/nicki/lib/share/perl5:/home/nicki/lib/perl5/:/home/nicki/lib/perl5/site_perl:; + +#execution of the linkYX pipeline +./runLinkYX.sh michalovova.monika@gmail.com misa + +echo "Copying of the output data started." `date` >>/storage/brno2/home/nicki/linkyx/log; + +#copying output files +cp -ar * /storage/brno2/home/nicki/linkyx_out; +#cleaning +rm -rf $SCRATCHDIR +trap "rm -rf $SCRATCHDIR" SIGTERM + diff -r 000000000000 -r 05c27700e5ca scripts/bam_analysis.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/bam_analysis.pl Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,116 @@ +#!/usr/bin/perl +#NOTE: The following code is adapted from the post http://www.biostars.org/p/44867/#44906 + +use strict; +use warnings; + +use Bio::DB::Sam; +open (MP, '>mpileup'); + +# all necessary inputs (I use Getopt::Long to obtain input parameters) +my $opt_i = $ARGV[0]; #"mother.bam"; # should have an index file named input.bam.bai +my $opt_f = $ARGV[1]; #"reference.fasta"; +my $chr_id = $ARGV[2]; #'comp1_c0_seq1'; # your chromosome-id +my $snp_pos = $ARGV[3]; # position you want to call all variants in this position +# create the object +my $sam = Bio::DB::Sam->new( -fasta => $opt_f, -bam => $opt_i ); + +# get all reads that cover this SNP -- therefore, start and end set to $snp_pos +my @alignments = $sam->get_features_by_location(-seq_id => $chr_id, -start => $snp_pos, -end => $snp_pos ); + + my $depth=@alignments; + print MP "DEPTH:".$depth."\n"; + +my %res; # output hash that'll contain the count of each available nucleotide (or blank if the read covering the SNP is spliced in this position). +# loop over all alignments +for my $cAlign (@alignments) { + # parameters we'll need from our bam file + + my $start = $cAlign->start; # get start coordinate + my $end = $cAlign->end; # get end coordinate + my $ref_seq = $cAlign->dna; # get reference DNA sequence + my $read_seq = $cAlign->query->dna; # get query DNA sequence + + #print $read_seq."\n"; + #print "start: ".$start." end: ".$end."\n"; + + my $cigar = $cAlign->cigar_str; # get CIGAR sequence + my $cigar_ref = $cAlign->cigar_array; # probably the important useful of all. splits cigar to array of array reference + + #print $cigar."\n"; # Ex: $cigar = 20M100N50M => $cigar_ref = [ [ 'M' 20 ] [ 'N' 100] ['M' 50] ] + + my $ref_cntr = $start; # $ref_cntr = assign start to counter variable for reference. This will ultimately + # keep track of the current position on the chromosome + my $read_cntr = 0; # $read_cntr = computes offset on the read + my $read_snp_pos = ""; # variable to hold base at $snp_pos from current read + + foreach my $deref ( @$cigar_ref ) { + my $cigar_chr = $deref->[0]; # cigar character (ex: M, N, I, D etc...) + my $len_chr = $deref->[1]; # number corresponding to `this` cigar character ( ex: 20, 100 ) + + # NOTE: I => insertion in to the reference, meaning the read has the base(s) but the REFERENCE fasta does NOT + # D => deletion from the reference, meaning the READ does NOT have the base(s), but the reference does + + # modify reference counter only on M, N or D occurrence + if( $cigar_chr eq "M" || $cigar_chr eq "N" || $cigar_chr eq "D") { + $ref_cntr += $len_chr; + } + + if( $cigar_chr eq "S" ) { + #print "soft_clipped.\n"; + } + + # modify offset only on M or I occurrence + if( $cigar_chr eq "M" || $cigar_chr eq "I" || $cigar_chr eq "S") { + $read_cntr += $len_chr; + } + + + # now, check if the current operation takes ref_cntr past the SNP position. If it does, + # 1) If the current operation is NOT "M", then its either "N" or "D". Both of them mean + # that the read doesn't have a base at the SNP. So, this read is either spliced or has + # a deletion at that point and is not useful for your SNP location. + # 2) If the current position IS "M", then the current operation has gotten is past SNP + # location. So, we FIRST SUBTRACT what we added in this operation for ref_cntr and read_cntr, + # and then just add the difference ($snp_pos - $ref_cntr + 1) + + #print "read_cntr: ".$read_cntr."\nref_cntr: ".$ref_cntr." cigar: ".$cigar_chr."\n"; + + if( $ref_cntr > $snp_pos ) { + if( $cigar_chr eq "M" || $cigar_chr eq "S") { + $ref_cntr -= $len_chr; + $read_cntr -= $len_chr; + + #print "backing\n"; + #print "read_cntr: ".$read_cntr."\nref_cntr: ".$ref_cntr."\n"; + + #IMPORTANT + my $pos = $snp_pos - $ref_cntr + $read_cntr; + + #print "SNP position: ".$snp_pos; + #print "position: ".$pos; + + $read_snp_pos = substr( $read_seq, $pos, 1 ); + + #print "This is what we add: ".$read_snp_pos."\n"; + } + # if $cigar_chr is "N" or "D", do nothing. $read_snp_pos is set to "" + + if( $cigar_chr eq "N" || $cigar_chr eq "D") { + print MP "NAN\n"; + } + + # add value of $read_snp_pos to hash and get out of loop - to next read + $res{$read_snp_pos}++; + last; + } + } +} + +#Here, I am just printing to output. +#print "Count\n"; +foreach my $key ( keys %res ) { + print MP "$key:$res{$key}\n"; +} +#print "--\n"; +close MP; diff -r 000000000000 -r 05c27700e5ca scripts/contains_these_variants.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/contains_these_variants.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,57 @@ +#!/bin/bash +#input example: perc% bam comp100134_c0_seq1 28 T C +#returns true if the alternative allele occurs in >= than perc (%) cases + +perc=$1; bam=$2; contig=$3; position=$4; ref=$5; alt=$6; + +echo contig $contig position $position ref $ref alt $alt >>kontrola; + +depth=0; + +perl ${LINKYX_PATH}/scripts/bam_analysis.pl $bam reference.fasta $contig $position; #writes to mpileup; +pro_hits=`grep -w "$alt" mpileup | cut -f2 -d":"`; + +if [ -z "$pro_hits" ]; then + hits=0; +else + hits=$pro_hits; +fi + +depth=`grep -w "DEPTH" mpileup | cut -f2 -d":"`; + +echo "hits: " $hits " depth: " $depth >>kontrola; + +if [[ $depth -eq $zero ]]; then + echo "0"; + exit; +fi + +if [ $depth -lt 5 ]; then + #depth <=4 + if [ $hits -gt 0 ]; then + echo "1"; #in this depth, none of variants can be tolerated + else + echo "0"; #ok + fi +else + if [ $depth -lt 25 ]; then + #depth 5..24 + if [ $hits -gt 1 ]; then + echo "1"; #in this depth, one variant can be tolerated + else + echo "0"; #ok + fi + else + #depth >=25 + hits=$[hits*100]; + percentage=`echo "scale=3; $hits/$depth" | bc`; + + if (( $(echo "$perc < $percentage"|bc -l) )); then + echo "1"; #too much of WRONG variants + else + echo "0"; #in tolerance + fi + fi +fi + + diff -r 000000000000 -r 05c27700e5ca scripts/createBamFromResults.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/createBamFromResults.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,16 @@ +#!/bin/bash +set -e; +#example usage: ./createBamFromResults list_of_sequences bam_file outfile reference +#creates small bam files containg only sex-linked genes and their corresponding reads + +list_of_sequences=$1; +bam_file=$2; +outfile=$3; +reference=$4 + +samtools view -h -o out.sam $bam_file; +grep -f $list_of_sequences out.sam >igv; +cat igv | sort -r >$outfile; +samtools view -bS $outfile | samtools sort - ${outfile%????}; + +rm -f igv out.sam; \ No newline at end of file diff -r 000000000000 -r 05c27700e5ca scripts/filter_diverged_Y_contigs.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/filter_diverged_Y_contigs.pl Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,140 @@ +#!/usr/bin/perl -w +use strict; + +my @inputs = @ARGV; +chomp(@inputs); + +my $reads_number_mother=$inputs[0]; +my $reads_number_father=$inputs[1]; +my $reads_number_daughter=$inputs[2]; +my $reads_number_son=$inputs[3]; +my $reference=$inputs[4]; +my $LINKYX_PATH=$inputs[5]; + +my $mother="statistics/stat_male_mother"; +my $father="statistics/stat_male_father"; +my $daughter="statistics/stat_male_daughter"; +my $son="statistics/stat_male_son"; + +open(MOTHER_FILE, $mother) or die "Impossible to open source file: $!\n"; +open(FATHER_FILE, $father) or die "Impossible to open source file: $!\n"; +open(DAUGHTER_FILE, $daughter) or die "Impossible to open source file: $!\n"; +open(SON_FILE, $son) or die "Impossible to open source file: $!\n"; + +my %hash = (); #contig <-> overall coverage hash + +my $mother_line; my $mother_cell; my @mother_cells; +my $father_line; my $father_cell; my @father_cells; +my $daughter_line; my $daughter_cell; my @daughter_cells; +my $son_line; my $son_cell; my @son_cells; + +my $check; +my $comp; my $contig; +my $comp1; my $comp2; my $comp3; my $comp4; my $comp_overall; my $count=0; my $coverage_check; my $girls_check; my $girls; + +print "read numbers: mother ".$reads_number_mother." father ".$reads_number_father." daughter ".$reads_number_daughter." son ".$reads_number_son."\n"; + +#variables to set +my $read_limit=15; #at least 15 reads +my $girl_limit=3; #each of the females can have 3 reads at most + + + while () { + + + $mother_line = $_; chomp($mother_line); + $father_line = ; chomp($father_line); + $daughter_line = ; chomp($daughter_line); + $son_line = ; chomp($son_line); + + #contig length - mapped - unmapped + #example: comp1260_c0_seq1 273 17 10 + @mother_cells = split("\t", $mother_line); $mother_cell=$mother_cells[2]; + @father_cells = split("\t", $father_line); $father_cell=$father_cells[2]; + @daughter_cells = split("\t", $daughter_line); $daughter_cell=$daughter_cells[2]; + @son_cells = split("\t", $son_line); $son_cell=$son_cells[2]; + + #contig being processed + $contig=$mother_cells[0]; + + #check if files are sorted the same way + $check=(($mother_cells[0] eq $father_cells[0]) eq ($daughter_cells[0] eq $son_cells[0])); + if ($check==1) { + #print "ok"; + } else { + die("Check input files, wrong order of contigs."); + } + + #normalization + $father_cell = $father_cell/($reads_number_father/$reads_number_mother); + $daughter_cell = $daughter_cell/($reads_number_daughter/$reads_number_mother); + $son_cell = $son_cell/($reads_number_son/$reads_number_mother); + + #minimal number of reads for males + $coverage_check=(($father_cell>=$read_limit) && ($son_cell>=$read_limit)); + + #for diverged Y-LINKED gene, males should have much greater coverage then females + + #mother must have less coverage than father and son + $comp1=$mother_cell<$father_cell; + $comp2=$mother_cell<$son_cell; + + #daughter must have less coverage than father and son + $comp3=$daughter_cell<$father_cell; + $comp4=$daughter_cell<$son_cell; + + #females have to have low overall number of reads + $girls_check=(($mother_cell<=$girl_limit) && ($daughter_cell<=$girl_limit)); + + #together, daughter and mother must be at most 1/3 of overall coverage + $girls=$mother_cell+$daughter_cell; my $guys=$father_cell+$son_cell; + + my $fraction; + if (($girls+$guys)>0) { + $fraction=$girls/($girls+$guys); + } else { + $fraction=0; + } + + $comp_overall=$fraction<0.03; + + #all conditions satisfied + $comp=$comp1 && $comp2 && $comp3 && $comp4 && $comp_overall && $coverage_check && $girls_check; + + #print contig name + if ($comp==1) { + #contig fulfilled all the criteria, added to hash + $count=$count+1; + $hash{ $contig } = $father_cell + $son_cell; + system("echo $contig >>Y_list"); + } + } + + my $iso; + foreach (sort {$hash{$b} <=> $hash{$a}} keys %hash) { + print "$_ $hash{$_}\n\n"; + + #get sequence for each contig; + system("perl ${LINKYX_PATH}/scripts/get_sequences_based_on_ids.pl $reference $_"); + + $iso = `bash $LINKYX_PATH/scripts/isoform_exists.sh $_ references/male_contig_names`; + + if ($iso eq '') { + print "No isoforms.\n"; + } else { + print "Isoforms exist:\n"; + print $iso; + } + print "----------\n"; + } + + print "Number of candidate diverged Y contigs found: ".$count."\n"; + + + + + + + + + diff -r 000000000000 -r 05c27700e5ca scripts/get_average_contig_coverage.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/get_average_contig_coverage.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,38 @@ +#!/bin/bash +#get_average_contig_coverage $perc $contig $bam +#returns "1" -> #low coverage, "0" -> #in tolerance +perc=$1; contig=$2; bam=$3; reference=$4; + +pro_coverage=`samtools mpileup -f $reference -r $contig $bam | cut -f 4 | awk '{s+=$1}END{print s}' 2>/dev/null`; + +if [ -z "$pro_coverage" ]; then + coverage=0; +else + coverage=$pro_coverage; +fi + +pro_positions=`samtools mpileup -f $reference -r $contig $bam | wc -l 2>/dev/null` + +if [ -z "$pro_positions" ]; then + positions=0; +else + positions=$pro_positions; +fi + +if [[ $positions -eq $zero ]]; then + echo "1"; + exit; +fi + + +average_coverage=`echo "scale=3; $coverage/$positions" | bc`; + + if (( $(echo "$average_coverage < $perc"|bc -l) )); then + echo "1"; #low coverage + else + echo "0"; #in tolerance + fi + + + + diff -r 000000000000 -r 05c27700e5ca scripts/get_sequence_based_on_id.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/get_sequence_based_on_id.pl Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,14 @@ +use Bio::DB::Fasta; + +my $fastaFile = shift; +my $queryFile = shift; + +my $db = Bio::DB::Fasta->new( $fastaFile ); + $seq = $queryFile; + chomp($queryFile); + + my $sequence = $db->seq($seq); + if (!defined( $sequence )) { + die "Sequence $seq not found. \n" + } + print ">$seq\n", "$sequence\n"; \ No newline at end of file diff -r 000000000000 -r 05c27700e5ca scripts/get_sequences_based_on_ids.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/get_sequences_based_on_ids.pl Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,16 @@ +use Bio::DB::Fasta; + +my $fastaFile = shift; +my $queryFile = shift; + +my $db = Bio::DB::Fasta->new( $fastaFile ); +open (IN, $queryFile); +while (){ + chomp; + $seq = $_; + my $sequence = $db->seq($seq); + if (!defined( $sequence )) { + die "Sequence $seq not found. \n" + } + print ">$seq\n", "$sequence\n"; +} \ No newline at end of file diff -r 000000000000 -r 05c27700e5ca scripts/isoform_exists.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/isoform_exists.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,6 @@ +#!/bin/bash +#we will search for isoforms of this contig +contig_to_search=$1; +reference=$2; +#including only putative isoforms +part=`echo $contig_to_search | sed -n "s/^\(.*\_c[0-9]\+\)\_seq[0-9]\+/\1/p"`; egrep "$part\_" $reference | grep -v $contig_to_search; \ No newline at end of file diff -r 000000000000 -r 05c27700e5ca scripts/number_of_not_uniq_mapped_reads.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/number_of_not_uniq_mapped_reads.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,53 @@ +#!/bin/bash +#sort_into_categories $contig +#family member with the biggest number of not uniquely mapped reads reported + +dir=$1; +contig=$2; + +all_unmapped1=`grep $contig statistics/stat_mother | cut -f 3`; +high_qual_unmapped1=`grep $contig statistics/stat_mother_high | cut -f 3`; +diff_mother1=`expr $all_unmapped1 - $high_qual_unmapped1`; +percentage1=`echo "scale=3; $diff_mother1/$all_unmapped1*100" | bc`; + +all_unmapped2=`grep $contig statistics/stat_father | cut -f 3`; +high_qual_unmapped2=`grep $contig statistics/stat_father_high | cut -f 3`; +diff_mother2=`expr $all_unmapped2 - $high_qual_unmapped2`; +percentage2=`echo "scale=3; $diff_mother2/$all_unmapped2*100" | bc`; + +all_unmapped3=`grep $contig statistics/stat_daughter | cut -f 3`; +high_qual_unmapped3=`grep $contig statistics/stat_daughter_high | cut -f 3`; +diff_mother3=`expr $all_unmapped3 - $high_qual_unmapped3`; +percentage3=`echo "scale=3; $diff_mother3/$all_unmapped3*100" | bc`; + +all_unmapped4=`grep $contig statistics/stat_son | cut -f 3`; +high_qual_unmapped4=`grep $contig statistics/stat_son_high | cut -f 3`; +diff_mother4=`expr $all_unmapped4 - $high_qual_unmapped4`; +percentage4=`echo "scale=3; $diff_mother4/$all_unmapped4*100" | bc`; + +#searching for maximum - family member that has the biggest number of NOT uniquely mapped reads + if (( $(echo "$percentage1 > $percentage2"|bc -l) )); + then + max1="$percentage1"; + else + max1="$percentage2"; + fi + + if (( $(echo "$percentage3 > $percentage4"|bc -l) )); + then + max2="$percentage3"; + else + max2="$percentage4"; + fi + + + if (( $(echo "$max1 > $max2"|bc -l) )); + then + percentage="$max1"; + else + percentage="$max2"; + fi + +echo $percentage; + + diff -r 000000000000 -r 05c27700e5ca scripts/prepare_statistics.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/prepare_statistics.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,26 @@ +#!/bin/bash +set -e; + +#variables +mkdir -p scripts/statistics; #create directory if it doesn't exist + +echo "Calculation of statistics started." + +#get statistics about mapped and unmapped reads for every contig + + idxstats_bam_file () + { + for ARG in "$@"; + do + samtools idxstats bam/aln_cleaned_sorted_deduplicated_${ARG}_male.bam >scripts/statistics/stat_${ARG} & + done; + } + + idxstats_bam_file mother father daughter son; + +wait; +echo "Idxstats successfully created." + + + + diff -r 000000000000 -r 05c27700e5ca scripts/sorting.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/sorting.pl Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,38 @@ +#!/usr/bin/perl -w +use strict; +#usage: perl sorting.pl A/ + +my @inputs = @ARGV; +chomp(@inputs); + +my $dir = $inputs[0]; +my $reference = $inputs[1]; +my $LINKYX_PATH = $inputs[2]; +my $results = "X_results.txt"; +my %hash = (); #contig <-> family member with the maximal number of not uniquely mapped reads +my $contig; my $count=0; my $iso; + +open(RESULTS_FILE, $results) or die "(sorting.pl) Impossible to open source file: $!\n"; + + while () { + $contig = $_; chomp($contig); + $count = `bash $LINKYX_PATH/scripts/number_of_not_uniq_mapped_reads.sh $dir $contig`; + $hash{$contig} = $count; + } + +foreach (sort {$hash{$a} <=> $hash{$b}} keys %hash) { + print "$_ $hash{$_}"; + + #get sequence + print "% of not uniquely mapped reads for contig ".$_.": ".$hash{$_}."\n"; + system("perl $LINKYX_PATH/scripts/get_sequences_based_on_ids.pl $reference $_"); + + $iso = `bash $LINKYX_PATH/scripts/isoform_exists.sh $_ references/reference_contig_names`; + if ($iso eq '') { + print "No isoforms.\n"; + } else { + print "Isoforms exists:\n"; + print $iso; + } + print "----------\n"; + } \ No newline at end of file diff -r 000000000000 -r 05c27700e5ca scripts/test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/test.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,24 @@ +#!/bin/bash +#example usage: ./test.sh comp100628_c0_seq1 5 A/contig_pos_ref_alt_father mother.bam + +contig_to_check=$1 +percentage=$2 +forbidden=$3 +bam=$4 +dir=$5; + +hits=0; + +grep $contig_to_check $forbidden | (while read line; do + + #tresholds described in table 1C + result=`bash ${LINKYX_PATH}/scripts/contains_these_variants.sh $percentage $bam ${line}` + + echo "result: " $result >>kontrola; + hits=$(($hits + $result)) + echo "hits: " $hits >>kontrola; +done; + +echo $hits; +) + diff -r 000000000000 -r 05c27700e5ca scripts/to_get_Y_variants.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/to_get_Y_variants.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,104 @@ +#!/bin/bash +set -e; + +#read config variables +echo "Reading config...." >&2 +#echo `ls -l` +computer_name=`hostname`; +if [ $computer_name == "misa" ]; then + #local_computer + source config_devel; +else + #metacentrum machine + source config_meta; +fi + +#files needed: reference_male.fasta $reads_1 $reads_2 + +reference=$1; +reads_1="input/$2"; echo "reads_1: " $reads_1; +reads_2="input/$3"; echo "reads_2: " $reads_2; +name=$4; +fragments=$5; + +#INDEXING FILES + +if [ -e "references/reference_male.dict" ]; +then + echo "Reference exists. Not being created again."; +else + echo "seconds of run: $SECONDS"; + java -jar $CreateSequenceDictionary R=$reference O=references/reference_male.dict >mlogfile 2>>errlogfile; + echo "0/9 INDEXING FILES successful"; + echo "seconds of run: $SECONDS"; +fi + +if [ -e "references/reference_male.fai" ]; +then + echo "Samtools reference exists. Not being created again."; +else + echo "seconds of run: $SECONDS"; + echo "reference:"$reference; + samtools faidx $reference 2>>errlogfile; + echo "0/9 INDEXING FILES successful"; + echo "seconds of run: $SECONDS"; +fi + +#1 MAPPING WITH BWA +bwa index $reference >>mlogfile 2>>errlogfile; + +#differs based on the fact whether reads are single or paired-end +bwa aln -t 2 $reference $reads_1 > bam/aln_sa1_${name}_male.sai & 2>>errlogfile; +wait; + +if [[ $fragments =~ (single) ]]; then + #single end reads + bwa samse $reference bam/aln_sa1_${name}_male.sai $reads_1 > bam/aln_${name}_male.sam 2>>errlogfile; + echo "bwa samse $reference bam/aln_sa1_${name}_male.sai $reads_1 > bam/aln_${name}_male.sam 2>>errlogfile"; +else + #pair-end reads + bwa aln -t 2 $reference $reads_2 > bam/aln_sa2_${name}_male.sai & 2>>errlogfile; + echo "bwa aln -t 2 $reference $reads_2 > bam/aln_sa2_${name}_male.sai & 2>>errlogfile"; + wait; + bwa sampe $reference bam/aln_sa1_${name}_male.sai bam/aln_sa2_${name}_male.sai $reads_1 $reads_2 > bam/aln_${name}_male.sam 2>>errlogfile; + echo "bwa sampe $reference bam/aln_sa1_${name}_male.sai bam/aln_sa2_${name}_male.sai $reads_1 $reads_2 > bam/aln_${name}_male.sam 2>>errlogfile"; +fi + +wait; +rm -f bam/aln_sa1_${name}_male.sai bam/aln_sa2_${name}_male.sai + + +echo "1/6 MAPPING WITH BWA successful"; +echo "seconds of run: $SECONDS"; + +#2 CLEANING FILES - adjust MAPQ scores +echo "$SECONDS"; +java -jar $CleanSam I=bam/aln_${name}_male.sam O=bam/aln_cleaned_${name}_male.sam 2>>/dev/null; +echo "2/6 CLEANING FILES - adjust MAPQ scores successful"; +echo "seconds of run: $SECONDS"; +wait + +#3 CONVERTING TO BAM FILE +samtools view -bS bam/aln_cleaned_${name}_male.sam > bam/aln_cleaned_${name}_male.bam 2>>errlogfile; +echo "3/6 CONVERTING TO BAM FILE successful"; +echo "seconds of run: $SECONDS"; +wait + +#4 SORTING BAM FILE +samtools sort bam/aln_cleaned_${name}_male.bam bam/aln_cleaned_sorted_${name}_male >mlogfile 2>>errlogfile; +echo "4/6 SORTING BAM FILE successful"; +echo "seconds of run: $SECONDS"; +wait; + +#5 REMOVING DUPLICATES +java -jar $MarkDuplicates INPUT=bam/aln_cleaned_sorted_${name}_male.bam OUTPUT=bam/aln_cleaned_sorted_deduplicated_${name}_male.bam METRICS_FILE=picard_info.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 2>>/dev/null; +echo "5/6 REMOVING DUPLICATES successful"; +echo "seconds of run: $SECONDS"; +wait; + +#9 REMOVING FILES +rm -f bam/aln_${name}_male.sam bam/aln_cleaned_${name}_male.sam bam/aln_cleaned_${name}_male.bam bam/aln_cleaned_sorted_${name}_male.bam >>mlogfile 2>>errlogfile; +echo "6/6 REMOVING FILES successful"; +echo "seconds of run: $SECONDS"; +echo "DONE"; + diff -r 000000000000 -r 05c27700e5ca scripts/to_get_vcf_files.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/to_get_vcf_files.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,113 @@ +#!/bin/bash +set -e; + +#read config variables +echo "Reading config...." >&2 +#echo `ls -l` +computer_name=`hostname`; +if [ $computer_name == "misa" ]; then + #local_computer + source config_devel; +else + #metacentrum machine + source config_meta; +fi + +#files needed: reference.fasta $reads_1 $reads_2 + +reference=$1; +reads_1="input/$2"; echo "reads_1: " $reads_1; +reads_2="input/$3"; echo "reads_2: " $reads_2; +name=$4; +fragments=$5; + +echo "reference:" $reference "reads 1:" $reads_1 "reads 2:" $reads_2 "name:" $name; + +#INDEXING FILES + +if [ -e "references/reference.dict" ]; +then + echo "Picard reference exists. Not being created again." +else + echo "seconds of run: $SECONDS" + echo "reference:"$reference; + java -jar $CreateSequenceDictionary R=$reference O=references/reference.dict >mlogfile 2>>errlogfile + echo "0/9 INDEXING FILES successful" + echo "seconds of run: $SECONDS" +fi + +if [ -e "references/reference.fai" ]; +then + echo "Samtools reference exists. Not being created again." +else + echo "seconds of run: $SECONDS" + echo "reference:"$reference; + samtools faidx $reference 2>>errlogfile; + echo "0/9 INDEXING FILES successful" + echo "seconds of run: $SECONDS" +fi + +#1 MAPPING WITH BWA +bwa index $reference >>mlogfile 2>>errlogfile + +#differs based on the fact wheter reads are single or paired-end +bwa aln -t 2 $reference $reads_1 > bam/aln_sa1_$name.sai & 2>>errlogfile +wait; + +if [[ $fragments =~ (single) ]]; then + #single-end reads + bwa samse $reference bam/aln_sa1_$name.sai $reads_1 > bam/aln_$name.sam 2>>errlogfile + echo "bwa samse $reference bam/aln_sa1_$name.sai $reads_1 > bam/aln_$name.sam 2>>errlogfile"; + wait; +else + #pair-end reads + bwa aln -t 2 $reference $reads_2 > bam/aln_sa2_$name.sai & 2>>errlogfile + echo "bwa aln -t 2 $reference $reads_2 > bam/aln_sa2_$name.sai & 2>>errlogfile"; + wait; + bwa sampe $reference bam/aln_sa1_$name.sai bam/aln_sa2_$name.sai $reads_1 $reads_2 > bam/aln_$name.sam 2>>errlogfile + echo "bwa sampe $reference bam/aln_sa1_$name.sai bam/aln_sa2_$name.sai $reads_1 $reads_2 > bam/aln_$name.sam 2>>errlogfile"; +fi + +wait; +rm -f bam/aln_sa1_$name.sai bam/aln_sa2_$name.sai + +echo "1/7 MAPPING WITH BWA successful" +echo "seconds of run: $SECONDS" + +#2 CLEANING FILES - adjust MAPQ scores +echo "$SECONDS" +java -jar $CleanSam I=bam/aln_$name.sam O=bam/aln_cleaned_$name.sam 2>>/dev/null +echo "2/7 CLEANING FILES - adjust MAPQ scores successful" +echo "seconds of run: $SECONDS" +wait + +#3 CONVERTING TO BAM FILE +samtools view -bS bam/aln_cleaned_$name.sam > bam/aln_cleaned_$name.bam 2>>errlogfile +echo "3/7 CONVERTING TO BAM FILE successful" +echo "seconds of run: $SECONDS" +wait + +#4 SORTING BAM FILE +samtools sort bam/aln_cleaned_$name.bam bam/aln_cleaned_sorted_$name >mlogfile 2>>errlogfile +echo "4/7 SORTING BAM FILE successful" +echo "seconds of run: $SECONDS" +wait +#rm aln.bam aln_cleaned.bam + +#5 REMOVING DUPLICATES +java -jar $MarkDuplicates INPUT=bam/aln_cleaned_sorted_$name.bam OUTPUT=bam/aln_cleaned_sorted_deduplicated_$name.bam METRICS_FILE=picard_info.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 2>>/dev/null +echo "5/7 REMOVING DUPLICATES successful" +echo "seconds of run: $SECONDS" +wait; + +#6 SNP AND VARIANT CALLING +samtools mpileup -uf $reference bam/aln_cleaned_sorted_deduplicated_$name.bam | $bcftools view -p 0.85 -cgv - | $vcfutils varFilter >vcf/aln_0.85_$name.vcf 2>>errlogfile +echo "6/7 SNP AND VARIANT CALLING successful" +echo "seconds of run: $SECONDS" + +#7 REMOVING FILES +rm -f bam/aln_$name.sam bam/aln_cleaned_$name.sam bam/aln_cleaned_$name.bam bam/aln_cleaned_sorted_$name.bam >>mlogfile 2>>errlogfile +echo "7/7 REMOVING FILES successful" +echo "seconds of run: $SECONDS" +echo "DONE" + diff -r 000000000000 -r 05c27700e5ca tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,65 @@ + + + $REPOSITORY_INSTALL_DIR + + + + + + http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2 + sed -i 's/O2/O2 -fPIC/' Makefile + make + + $INSTALL_DIR + $INSTALL_DIR + + + + Compiling samtools with fPIC in order to create bam.h and compiled libbam.a files + + + + + + + + + + XML::Parser + http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz + Bio::DB::Fasta + File::Slurp + Bio::DB::Sam + + + + + Bundle::BioPerl + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r 000000000000 -r 05c27700e5ca vcf/.gitignore diff -r 000000000000 -r 05c27700e5ca vcf/daughter.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcf/daughter.vcf Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,40 @@ +##fileformat=VCFv4.1 +##samtoolsVersion=0.1.19-44428cd +##reference=file:///Users/alice/programs/galaxy/galaxy-dist/database/files/000/dataset_340.dat +##contig= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /Users/alice/programs/galaxy/galaxy-dist/database/files/000/dataset_343.dat +comp0_c0_seq1 672 . 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DP=22;VDB=1.304866e-01;RPB=-1.001671e+00;AF1=0.5;AC1=1;DP4=0,13,0,9;MQ=57;FQ=99;PV4=1,0.2,0.18,1 GT:PL:GQ 0/1:126,0,165:99 diff -r 000000000000 -r 05c27700e5ca vcf/father.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcf/father.vcf Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,40 @@ +##fileformat=VCFv4.1 +##samtoolsVersion=0.1.19-44428cd +##reference=file:///Users/alice/programs/galaxy/galaxy-dist/database/files/000/dataset_340.dat +##contig= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /Users/alice/programs/galaxy/galaxy-dist/database/files/000/dataset_339.dat +comp0_c0_seq1 672 . A C 99.5 . 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