| Next changeset 1:01a241476407 (2017-03-02) |
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Commit message:
planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4 |
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added:
CHANGE metaspades.xml spades.pl test-data/ecoli_1K_1.fq test-data/ecoli_1K_2.fq test-data/reference_1K.fa tool_dependencies.xml |
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| diff -r 000000000000 -r e93c1a0678cd CHANGE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CHANGE Tue Aug 09 10:46:28 2016 -0400 |
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| @@ -0,0 +1,4 @@ +1.0 +=== + - Supports SPades 3.9 + - CHANGE: Improved memory consumption in metagenomic pipeline. |
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| diff -r 000000000000 -r e93c1a0678cd metaspades.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metaspades.xml Tue Aug 09 10:46:28 2016 -0400 |
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| @@ -0,0 +1,140 @@ +<tool id="metaspades" name="metaspades" version="1.0"> + <description>genome assembler for metagenomics datasets</description> + <requirements> + <requirement type="package" version="3.9.0">spades</requirement> + </requirements> + <command interpreter="perl">spades.pl + $out_contigs + $out_contig_stats + $out_scaffolds + $out_scaffold_stats + $out_log + + ## if the first fileset is a paired-collection, use the key as the name + #if $files[0].file_type.type == "paired-collection": + $files[0].file_type.fastq_collection.name + #else: + NODE + #end if + ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output + spades.py + ## Forces unzipped output, faster + --disable-gzip-output + --meta + $onlyassembler + + -t \${GALAXY_SLOTS:-16} + + #if not $kmer_choice.auto_kmer_choice: + -k "$kmer_choice.kmers" + #end if + + ## Sequence files + #set num=1 + #if str( $lib_type ) == "paired_end": + #set prefix = 'pe' + #end if + --$prefix$num-$orientation + #for $file in $files + #if $file.file_type.type == "separate" + --$prefix$num-1 fastq:$file.file_type.fwd_reads + --$prefix$num-2 fastq:$file.file_type.rev_reads + #elif $file.file_type.type == "interleaved" + --$prefix$num-12 fastq:$file.file_type.interleaved_reads + #elif $file.file_type.type == "paired-collection" + --$prefix$num-1 fastq:$file.file_type.fastq_collection.forward + --$prefix$num-2 fastq:$file.file_type.fastq_collection.reverse + #end if + #end for + + + </command> + <inputs> + <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" /> + <conditional name="kmer_choice"> + <param name="auto_kmer_choice" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Automatically choose k-mer values" help="k-mer choices can be chosen by SPAdes instead of being entered manually" /> + <when value="false"> + <param name="kmers" type="text" label="K-mers to use, separated by commas" value="21,33,55" help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." /> + </when> + <when value="true"> </when> + </conditional> + + <!-- Reads --> + + <param name="lib_type" type="select" label="Library type"> + <option value="paired_end">Paired-end</option> + </param> + <param name="orientation" type="select" label="Orientation"> + <option value="fr" selected="true">-> <- (fr)</option> + <option value="rf"><- -> (rf)</option> + <option value="ff">-> -> (ff)</option> + </param> + <repeat name="files" title="Files" min="1"> + <conditional name="file_type"> + <param name="type" type="select" label="Select file format"> + <option value="separate">Separate input files</option> + <option value="interleaved">Interleaved files</option> + <option value="paired-collection">Paired List Collection</option> + </param> + <when value="separate"> + <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" /> + <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" /> + </when> + <when value="interleaved"> + <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" /> + </when> + <when value="paired-collection"> + <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" help="FASTQ format" /> + </when> + </conditional> + </repeat> + + + </inputs> + <outputs> + <data name="out_contigs" format="fasta" label="SPAdes contigs (fasta)" /> + <data name="out_contig_stats" format="tabular" label="SPAdes contig stats" /> + <data name="out_scaffolds" format="fasta" label="SPAdes scaffolds (fasta)" /> + <data name="out_scaffold_stats" format="tabular" label="SPAdes scaffold stats" /> + <data name="out_log" format="txt" label="SPAdes log" /> + </outputs> + <tests> + <test> + <param name="sc" value="false" /> + <param name="careful" value="false" /> + <param name="kmers" value="33,55" /> + <param name="lib_type" value="paired_end" /> + <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" /> + <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" /> + <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" /> + </test> + </tests> + <help> +**What it does** + +SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes. + +This wrapper runs SPAdes 3.9, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage. + +**License** + +SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2. + +This wrapper is copyrighted by Philip Mabon and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + +This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + +You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/. + +** Acknowledgments ** + +Original wrapper developed by Lionel Guy. + +Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes. + +Nicola Soranzo fixed various bugs. + </help> + <citations> + <citation type="doi">10.1089/cmb.2012.0021</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r e93c1a0678cd spades.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spades.pl Tue Aug 09 10:46:28 2016 -0400 |
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| @@ -0,0 +1,124 @@ +#!/usr/bin/env perl +## A wrapper script to call spades.py and collect its output +use strict; +use warnings; +use File::Temp qw/ tempfile tempdir /; +use File::Copy; +use Getopt::Long; + +# Parse arguments +my ($out_contigs_file, + $out_contigs_stats, + $out_scaffolds_file, + $out_scaffolds_stats, + $out_log_file, + $new_name, + @sysargs) = @ARGV; + + +my $output_dir = 'output_dir'; + +# Create log handle +open my $log, '>', $out_log_file or die "Cannot write to $out_log_file: $?\n"; + +# Run program +runSpades(@sysargs); +collectOutput($new_name); +extractCoverageLength($out_contigs_file, $out_contigs_stats); +extractCoverageLength($out_scaffolds_file, $out_scaffolds_stats); +print $log "Done\n"; +close $log; +exit 0; + +# Run spades +sub runSpades { + my $cmd = join(" ", @_) . " -o $output_dir"; + my $return_code = system($cmd); + if ($return_code) { + print $log "Failed with code $return_code\nCommand $cmd\nMessage: $?\n"; + die "Failed with code $return_code\nCommand $cmd\nMessage: $?\n"; + } + return 0; +} + +# Collect output +sub collectOutput{ + my ($new_name) = @_; + + # To do: check that the files are there + # Collects output + if ( not -e "$output_dir/contigs.fasta") { + die "Could not find contigs.fasta file\n"; + } + if ( not -e "$output_dir/scaffolds.fasta") { + die "Could not find scaffolds.fasta file\n"; + } + + #if a new name is given for the contigs and scaffolds, change them before moving them + if ( $new_name ne 'NODE') { + renameContigs($new_name); + } + else { + move "$output_dir/contigs.fasta", $out_contigs_file; + move "$output_dir/scaffolds.fasta", $out_scaffolds_file; + } + + + + open LOG, '<', "$output_dir/spades.log" + or die "Cannot open log file $output_dir/spades.log: $?"; + print $log $_ while (<LOG>); + return 0; +} + +#Change name in contig and scaffolds file +sub renameContigs{ + my ($name) = @_; + + open my $in, '<',"$output_dir/contigs.fasta" or die $!; + open my $out,'>', $out_contigs_file; + + while ( my $line = <$in>) { + #remove the NODE_ so we can rebuilt the display_id with our contig name with the contig number. + #also move the remainder of the length + if ( $line =~ />NODE_(\d+)_(.+)/) { + $line = ">$name" . "_$1 $2\n"; + } + print $out $line; + } + close $in; + close $out; + + + open $in, '<',"$output_dir/scaffolds.fasta" or die $!; + open $out,'>', $out_scaffolds_file; + + while ( my $line = <$in>) { + #remove the NODE_ so we can rebuilt the display_id with our contig name with the contig number. + #also move the remainder of the length + if ( $line =~ />NODE_(\d+)_(.+)/) { + $line = ">$name" . "_$1 $2\n"; + } + print $out $line; + } + close $in; + close $out; + +} + + +# Extract +sub extractCoverageLength{ + my ($in, $out) = @_; + open FASTA, '<', $in or die $!; + open TAB, '>', $out or die $!; + print TAB "#name\tlength\tcoverage\n"; + while (<FASTA>){ + next unless /^>/; + chomp; + die "Not all elements found in $_\n" if (! m/^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*)/); + my ($name,$n, $l, $cov) = ($1,$2, $3, $4); + print TAB "$name" . "_$n\t$l\t$cov\n"; + } + close TAB; +} |
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| diff -r 000000000000 -r e93c1a0678cd test-data/ecoli_1K_1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ecoli_1K_1.fq Tue Aug 09 10:46:28 2016 -0400 |
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| b'@@ -0,0 +1,8216 @@\n+@EAS20_8_6_1_9_1972/1 trim=6\n+ACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCG\n++\n+HHHHHHGHHHHFHHGGHHFHHHHHFHHFHFHHHHHFHHHHHFHHHHHHHHFHHFHFDHHGG@BGGHCDHE:;3)7.A973A:AA5>AD9G=D<D\n+@EAS20_8_6_1_163_1521/1\n+GCAGAAAACGTTCTGCATTTGCCACTGATGTACCGCCGAACTTCAACACTCGCATGGTTGTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCGCACTG\n++\n+HGHHIHHHDHHHHHIHHIHHHHHHHHHBHHHHHFHCFHHHHHHHGHHHHHEHHFHHHGHHIHHHGHGHHHIHFHHHHHGH?5<<;BD>6>?BGEHHGHFG\n+@EAS20_8_6_1_178_1948/1\n+ATTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAACAGTAACGTTGTGACCGCGCGCTTCTAATACGCCGGCCATAATGGCGATCGA\n++\n+GHHHHHHHHHGGHHHHHHGHHHHHHHEHHHHHHHHHHHHHFHHHEHHHHHHHFHFHIHHIHHHIHHHGHIIGGHBGGGHHFFGBHIFFGCIGGEFDG@AG\n+@EAS20_8_6_1_318_1522/1 trim=5\n+AAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCAC\n++\n+HHHHHHHHHHIHHHHHHHHHHHHHHHHHGEHHHHHEHHHHHHIHHHHGHHEHHGHBHDDEHHEGH?HEGGGIHDIGFFFEHE;EE;=AFE;AB/B\n+@EAS20_8_6_1_348_1372/1\n+AAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAAC\n++\n+HHHHHHHHHHHHHHHHHHHEHHGHHIHHHDHHHHHHHHHHFHHHGHHFHHH@HHHFHHHEHH<HH?@D>DHDEBEEGDFDCHECGB:?43CCCFG?90<6\n+@EAS20_8_6_1_389_646/1 trim=2\n+ACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAAC\n++\n+HBHGGHHIGHHHGDHHGHHDHHHGDHFGGHHHHHHHHHHHHIHHGFGHHHHHGHGGHGGDHHEFHDDHGGGHHH=HDDB9FHGGEIEHICEB?DBBAE\n+@EAS20_8_6_1_513_951/1\n+TTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGG\n++\n+HHHHHDHHHHHHIHGHGIEEDFHBDDHGGGBC?C?IHD>GFHGHG?DDGEB?;?,DCF=D??F=BDBGE=DDGDG.>76?>EB>54+?;=5;BEBDAGGA\n+@EAS20_8_6_1_530_1080/1 trim=1\n+AAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAG\n++\n+EHHHHHHGHHFEHHHHHGHHHHHHGHH=BHHHEHHHHHHHEHFEEHHFDHHHHHHFGHHHHFHFHHEHFHFEHEEHB>EG=F?E=>FHE@CH5HB:81@\n+@EAS20_8_6_1_546_406/1\n+AAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCAT\n++\n+HHHHHHGGGHHHHHHHHHHHHHIHHHHHHHHHHHHIFHHHHHHHHHHHIFHHHHHHHHHHHHHGHHHHFHHHHFHHHHEHHDH@8GFHHGHEFBHHGG5G\n+@EAS20_8_6_1_553_1132/1 correct\n+CGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACATGTTTTATTTGGGCAAATTCCTGATCGACGAAAGTTTTCAATTGCGCCAG\n++\n+HHHHHIHHHHHHGHHHHHHHHHDHHHHHHHHHHHIGHH@HHHHHGHHFHDHHHHHHHHGGGHH=HDHHHFHHHGHHHFHH55445#A@@:55555EGGDE\n+@EAS20_8_6_1_594_142/1 trim=11\n+GGTTGTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCGCACTGTCAGGTGCGGGCTTTTTTCTGTGTTTCCTGTACGCGTCAGCCCG\n++\n+HIHHHHHHHHHHHHHHHHHHHHHIHHFHDHHGEBEEEHHGHIIHHFHHEG@FAFHD;DEFHHH@E.:82=??:=:F5?E6;4<:@B?AE\n+@EAS20_8_6_1_641_1277/1 trim=50\n+GGGCTTTTTTCTGTGTTTCCTGTACGCGTCAGCCCGCACCGTTACCTGTG\n++\n+HHE=GHHHHHECGHHHG@FDHEFF7@@CAA?FA>FA?9;;>@;5=1AA+D\n+@EAS20_8_6_1_660_979/1 trim=5\n+AGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAAT\n++\n+HHEGHHHHHHHHHHHHHHHHGFFHHHFEEAHEHHGHHEHDFGHIHHHGGD<9F:FHFHHBC4EEEDEBGHHGE@BCBEDGGFFGACFG=4C39:B\n+@EAS20_8_6_1_763_241/1 trim=42\n+TTGTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCGCACTGTCAGGTGCGGGCTTT\n++\n+GHHHIG@HHHHHHGHGIHHHHHHHEDDFEHCBGGHHHHH@HFFGGAGE;B+>3223;D\n+@EAS20_8_6_1_789_699/1\n+GCGAGTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGCCACCAGGT\n++\n+HGHHHHHHHHGHF@GHHGHHFHF@FD??F>CDHHFHHHHHBEFHHAHCHHHEHH@HHHDFHH;HGHGFHHF>1DDFF?FFEHFEHF0AE.2061585=@/\n+@EAS20_8_6_1_802_355/1 correct\n+AGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGAT\n++\n+HIHHHHHHIGHDHHHHH#HHFDFBB?DDA>EFGDFHHFHFHHHHHHHEGFHHHFGHBH=;FF@;FEGHHHHHFHCHHEHDFHEHHFHDH=?HEFEHEHAH\n+@EAS20_8_6_1_807_1707/1 trim=15\n+TCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGCCACCAGGTGGTTGGTGATTTTGGCGG\n++\n+FHCEHGFHHHHGEEHHHHGHHFFHFHGHHHGHGFHH=HFCHHHHHEHEHHDFHHFFHHHHAHHBHA4>C6?@=8>5FBBFE?EEB\n+@EAS20_8_6_1_918_1054/1 correct trim=10\n+AACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCA\n++\n+HHGHHHHHHHHHHHHHHHHHHHHEHHFHHHHGHHHEHHHFIHGHFHHHFHGGFHC>D1D<AFD:CGGGGAB=FCECE23B/#8>=DD:EC\n+@EAS20_8'..b'<@>@8BG9G9\n+@EAS20_8_6_100_346_1515/1\n+TAATACGCCGGCCATAATGGCGATCGACATTTTCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGC\n++\n+FGDHEHHHHHHGHHHHHHHHBG?GEHHDDGHHHDH@GEEH?CHHFF?FDFEEFHEEFHGHHFFHEIHHGBGGEGDIGFEDEHBEHGEAFHGFH@HGGA?H\n+@EAS20_8_6_100_434_840/1 trim=47\n+ACCTGCCATCAGCACCATGTGATCAGCCGGAATGCGGCTTGCCGCAATACGGC\n++\n+HGHHHGHHHHHHGGHHHGHHHEGFHHHFHHDGHHEHGGHE:5=>9-<<.-BGB\n+@EAS20_8_6_100_451_465/1 correct\n+CGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACC\n++\n+FHHEHHHGHHHHHGFDHHBHBBDDDHEHHHGHIHHDHHEHHHHHEFHHHHHHI@HE=@FBFFCC#HHDHHEHHHH@HGADFF,=FB@F?F?FB4F?F@BB\n+@EAS20_8_6_100_452_1846/1 correct\n+CGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTA\n++\n+HFHHEHHHGHEEFEHHHHHHHGFHHHHHDHFGHFHGHHGH@B5>BAEHEHFF#?;-54457HHFAFACEFFCFAFGGGECGEEG#@@@AAFGGCDBHEE=\n+@EAS20_8_6_100_723_1564/1\n+TCTAATACGCCGGCCATAATGGCGATCGACATTTTCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCAT\n++\n+HHHHHHGHGHHHHHHHHDHHHGGHGFFHD=DFHHHFHHGGHHFHHHHHHHHDHGGHHHCHEHHGHGFHHHHGEG3H@HEDHHGHHFGEGGGGFFFGEGAG\n+@EAS20_8_6_100_776_1749/1 trim=5\n+GGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAAT\n++\n+H,/E8;GH88;?8AA=CFHFCF/F7FE0EA@1.=;ACFF>C=HFFFD=D=HFBFH1FFFG>@CD;GGFGBGAGGF8HHHHHHEHIHEH8H??,<A\n+@EAS20_8_6_100_779_871/1 trim=20\n+GTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAA\n++\n+GHHGGHGHHHHHHHCHHHFHHHFHHHHDFHHEHGHHEDHF?GG@::FGCDCB6E@F6:F<BFAC?EDF-:FEHFB:226A\n+@EAS20_8_6_100_816_1759/1 correct trim=47\n+AAAAAGCCCGCACTGTCAGGTGCGGGCTTTTTTCTGTGTTTCCTGTACGCGTC\n++\n+#GGHHHBHCGHHHHB@>DA@0#?8>/:/<=FFF/@,3/444(555<5/?3A,A\n+@EAS20_8_6_100_993_1119/1\n+GTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACC\n++\n+?@FDBEFGF8BFGFGHHHHEHHHHEHBFHHHHGGHHH@HGFHHHDH5HB?GHDGDFDHEHIFHFHFFHFE?HDFCFGEHEGBE=HHGGGGGHFHHGGIEG\n+@EAS20_8_6_100_1153_966/1\n+AGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGC\n++\n+HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHDHHCHHHHGBFHHDHDHHHHFCHBHEGEHEHGGEHH@GEG8FFBEHFF:FBFDA+DFC;C3\n+@EAS20_8_6_100_1183_226/1 correct trim=26\n+TTGGGCAAATTCCTGATCGACGAAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCG\n++\n+CFCCF?DCCDHEGHFHHHHFFFHD@HGEHHHGHHHGHHFHHHHGEEH:H>HHHDCFF#EADA366=A0A+8<AA\n+@EAS20_8_6_100_1263_900/1 correct trim=1\n+AGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCAC\n++\n+HGHHHHHHIHHHIHFBD?BCHHHHHDGHHHHEHHFCHFHHBHEHHHFHHDHHFEHHHGH=HEFFFHH@CFHBHEHHBGHGBCDBGFDH<EAF#9F#?@A\n+@EAS20_8_6_100_1277_357/1 trim=5\n+ACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGCCACCAGGTGGTTGGTGATTTTGGCGGGGGCAG\n++\n+DEHHHHIEHHHHHHHHGIGHHHHHHHGHHHHEFEHHHHHHHHFEHHHHHHHHH@CGHGCHFHHE@FB<=F=FFFFFFDG;BFDFFGFEG@9B24C\n+@EAS20_8_6_100_1337_252/1 correct trim=16\n+GCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGG\n++\n+GBHHHHHHGGHHBHEG@BEHHDHAHGBHGHDGDDEH#EBEDBFDHHC2EDF9?@EEHHE?CCH=EHEGAGGGEE4AGA6E1G?F\n+@EAS20_8_6_100_1432_436/1 trim=3\n+GTAGATTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAACAGTAACGTTGTGACCGCGCGCTTCTAATACGCCGGCCATAATGG\n++\n+HHHHHIHHGGHDGHHHHHEGHHHGHHDHHHEHHGHHHHGHHFHGDGHHDHECHDEGGFGGFGFFBGGEGEG?GBGHEHB9EGEDGDAEDEDE?DFBF\n+@EAS20_8_6_100_1457_1209/1 correct trim=7\n+TTGGGCAAATTCCTGATCGACGAAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGTCAAAAGTTCGGCAAAAAT\n++\n+HGHFFDBCBD#BBFFEDDFCHGHHEHCHHHEHHHHHHEAHHHGHBDGHEHEEGHGEE@GGGGFG?5C;A5:0;A4988-/>8@5>;<-37<?B\n+@EAS20_8_6_100_1609_245/1\n+GGTGGCCACCTGCCCCTGCCTGGCATTGCTTTCCAGAATATCGGCAACACGCAGAAAACGTTCTGCATTTGCCACTGATGTACCGCCGAACTTCAACACT\n++\n+BCBBDFHHHHHHEHHHHGHHHHHHDHHHHHHHGHHHGIHHHHHEHIDHGGIHHHFGHFHHGHHBGFFHHHHFHHFHHGHHIHHEHGFF=HGFHHBFFGBH\n+@EAS20_8_6_100_1637_1332/1\n+TGGTGCTAATGCGTTTCATGGATGTTGTGTACTCTGTAATTTTTATCTGTCTGTGCGCTATGCCTATATTGGTTAAAGTATTTAGTGACCTAAGTCAATA\n++\n+FHFHHFGGHGHFHGHHGHHHFEHHHGFFDFHFHHHGEDCGHHHHHG9HDGHFHGHHHEHEFGF=GAHEHHFEGFFGEHFHHHHFHHEBE?HHFHEGFDHH\n' |
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| diff -r 000000000000 -r e93c1a0678cd test-data/ecoli_1K_2.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ecoli_1K_2.fq Tue Aug 09 10:46:28 2016 -0400 |
| b |
| b'@@ -0,0 +1,8216 @@\n+@EAS20_8_6_1_9_1972/2 correct\n+GGTGGCCACCTGCCCCTGCCTGGCATTGCTTTCCAGAATATCGGCAACACGCAGAAAACGTTCTGCATTTGCCACTGATGTACCGCCGAACTTCAACACT\n++\n+HFHHHGHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHGHHGHEHHHHHHEH;G?F<F?GDFF/EEFBD:DCHHH7A@?EEH@HH96:4F@#76=C@@\n+@EAS20_8_6_1_163_1521/2\n+GGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACG\n++\n+HHGGFHHGHHHHHHHGFHHHHHHHCGHFHFHFHHHHHHGHHGHHDHHIEGEDFEHHCHHHHGCCGF>GFEFEGGFGGEIG1ACBCF?CD1?CADCD.DFB\n+@EAS20_8_6_1_178_1948/2\n+ATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTG\n++\n+HGHIHHHIHGGHHHHGHHFHHFDHHHHHGHHBHHHHHHGGGHHHHHHHHHFHHHHGHHFHFEDHGDHH>HGEFCHHCHHH=GGHBEGFFHEGGD@HHEEH\n+@EAS20_8_6_1_318_1522/2\n+AGAATATCGGCAACACGCAGAAAACGTTCTGCATTTGCCACTGATGTACCGCCGAACTTCAACACTCGCATGGTTGTTACCTCGTTACCTTTGGTCGAAA\n++\n+IGHFHHHDEHGHHEHHHEGHDHHHGHHHHHHEHHHHHDHHHHHGHHHHEGFAEHDGHFHHFDHFGHHHIGHIEGHHGGHFGFAHGHGFEHDHEEEB7<3<\n+@EAS20_8_6_1_348_1372/2\n+GGGCGGCGGCGAGTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGC\n++\n+HHHHHH@HGHHEHGHGHHHHDHHHHFHEHDDHHDHHHEEHHDHHHBFHCEGEHGGGDHHE@EFDAHHGHEDFGG:FDB<>=BDG?D=3BB>G?GGEGGD;\n+@EAS20_8_6_1_389_646/2 trim=17\n+TGCCACTGATGTACCGCCGAACTTCAACACTCGCATGGTTGTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCGCACTGTC\n++\n+HGGGDHHHAHGHHHHGHIHHEHHHGHFHHHHHFHHEG=GHEEFEHEHHEEEDGHGHFHDFFFADDHHF:>0&D0A4?,?AE=?\n+@EAS20_8_6_1_513_951/2 correct\n+ATAACAGTAACGTTGTGACCGCGCGCTTCTAATACGCCGGCCATAATGGCGATCGACATTTTCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCG\n++\n+GHFHGHDHGHHHHHHFHHHEFHHHHHGHFHBHEHHHFDHHGGHHBEHHGHHHFFFBHHHHHGEGDHFIHHHHEEC?GEGDFE;<E+@5@>?E;=?#A)?=\n+@EAS20_8_6_1_530_1080/2\n+GAAAACGTTCTGCATTTGCCACTGATGTACCGCCGAACTTCAACACTCGCATGGTTGTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCGCACTGTCA\n++\n+D?D?DG;FAFFGDGFDF?F:>=DD>GGGGGDAD:D+DD>DDFAFFDGFG4FFFFC<FF>BGCG/CFF59AFBD6DG@BA1.53;-:9:FG::F-:><>96\n+@EAS20_8_6_1_546_406/2\n+CGGGTGGACTCAGCAATATCGACGGTAGATTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAACAGTAACGTTGTGACCGCGCGCTT\n++\n+HHHHEHHHHHHHIHHFHHHHHHHHHGHHHIHHHHHFGHHGHHHHHBHHGBHHEHGHCGGGGHAGHEGGGGHEDECGGFE8GGE=EGGC>FGE@DDECGDD\n+@EAS20_8_6_1_553_1132/2 trim=6\n+GGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCC\n++\n+HHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHEGHHHHHABGEEHHDHAGHDHGGHFFFGH@HDGGHGHEEFIIBFFFIEGD@EFG<E@EC<6B\n+@EAS20_8_6_1_594_142/2\n+AACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACC\n++\n+GGHHHHHHHHHFGHHHHHGHHHDGDHHHHHHHFH?EHHHHGDGEHHHHDHHHIHHGIHHEFFHHHHFGFHGEHCGGGEGA;HFH@DEFEBEEAHE??=?C\n+@EAS20_8_6_1_641_1277/2\n+GGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTA\n++\n+FFE?FEBFG?EHFHDHDFHDEHGAEEFGFHHH?GH;HAGGFF7AEHCCBH?0FG=2FAB4EHGB>BC0<?EE=9C=E;F;:;AAAA+,=,6E@2AC3?<>\n+@EAS20_8_6_1_660_979/2\n+CCATGCAGGACATGTTTTATTTGGGCAAATTCCTGATCGACGAAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGTCAAAA\n++\n+HDHHEFHH@FHHHEHHGGGGEEEHFFHHFGHHHHHGGHHDBFBF;FFFGFDFGGHHHHG<FHCHHA9=B?=G@@?EHED9F8DHEDD3EBC&GD3)-000\n+@EAS20_8_6_1_763_241/2\n+TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT\n++\n+HHFDFGHHHHHEHHCHHFGHBEEAGHBCGEGHHEHDHEHH=HHHHHHHHGHHDBFGHHDGBIHHHHCHEHBE>HHGHBHHFHEGEHGHBDEHEH=F:E??\n+@EAS20_8_6_1_789_699/2 correct trim=20\n+TGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCC\n++\n+H=BHHFAECGAHHHF<AF@FFEEEEHHHHFCHHHHHGHH=FEHHHEHH4E1DAA=FEG?AHDEH#*F;1/AA7(D<?)FF\n+@EAS20_8_6_1_802_355/2 correct\n+CTGTACGCGTCAGCCCGCACCGTTACCTGTGGTAATGGTGATGGTGGTGGTAATGGTGGTGCTAATGCGTTTCATGGATGTTGTGTACTCTGTAATTTTT\n++\n+HHHHHHHHHHHGGGGHHHHIHGGIHHHHGHHEAEBFFBCF=GGD?D@2C;?<6?BFBFF>BCCE?BBDGDBD>2HF?8?C?:19?0&5-#=:/;6DHGD>\n+@EAS20_8_6_1_807_1707/2 trim=1\n+GAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGG\n++\n+FCFF2FBBFBEHGHH?D=AAFDGGCCHHHHBHEEHDEFAFFGGGDGGABIGECHEBBBHFHHHDDFEGGEEFD=1=BDDDCCGEEDDJCBBDDE;BEAG\n+@EAS20_8_6_1_918_1054/2 correct\n+GCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGT'..b'6_100_346_1515/2\n+TGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTC\n++\n+AADA@BBFBDHCGGBHHHGHH=HEHFHHH@HFHHFFDHFE;HHEHGF<CGHHH@FGGG1F<B9BDHHHH=H?HE6GFADFEBHBDFD/BGF1F??HGHGF\n+@EAS20_8_6_100_434_840/2\n+AGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTAC\n++\n+HHHGHHFHGGHHEFHHH>FHHHHHFHFHHEHHHFFHHHHDHHGHHBAHHHFHHEHFHHGBIHHEFIFGEDGGC;FE80>ABC4CAEGG;A182;916>98\n+@EAS20_8_6_100_451_465/2 correct trim=22\n+GTTGCGTCCAAGCACCACCAGTTCGCCTTTTTCATTACCGGCGGTGAAACCTGCCATCAGCACCATGTGATCAGCCGG\n++\n+HIHHDHHHHGHIGHHHHGHHHFHHIHIHHHHHIHHHHHGIH@HH>A;AD95#+43=?C:35:6865/9;13=<:?B?C\n+@EAS20_8_6_100_452_1846/2 correct\n+CTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGA\n++\n+HHHHHGHHHHGHHHFHHHHGHGHDHHFHBEHHHFHFGHHGHHHDHE#HEDF?CF?DFD:E252+7CBF?14:*:AA;:C9;9;+ABAD8#64<::;3+<7\n+@EAS20_8_6_100_723_1564/2 correct trim=2\n+TGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTG\n++\n+HHHEHEHEH?HHEEHEEGHHBEFEEHHHFHHHHHHFHEHFEHHFHGHHGHED/EHDHEH@A88D@C(E6BEEHD@5?CE:AG;D@C;;2@>#8.95?C\n+@EAS20_8_6_100_776_1749/2\n+TCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACATGTTTTATTTGGGCAAATTCCTGATC\n++\n+F3G30CEG?GDD4D=H<8BFEF8HDGHHH1HHFFEHDHB1;5>;<8EDC8??@ADEHH@HEEEHFHHHHHHEHHHG:@FFFGA6AEHH@=EHH;HFC/FF\n+@EAS20_8_6_100_779_871/2\n+AAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTAAAG\n++\n+FGEFCEHFFFBHHFHHHHEEHHHBCFAFEHGHGHH7B@:EDFHDE5CAABBHCB7@8?A8?FB3BBADBDG>;;CF=FGGD52B0?A2A?;;=;BA5DAE\n+@EAS20_8_6_100_816_1759/2\n+AAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAAC\n++\n+63;=>>3>>?DECADBBDCG?@7?5DCEEEGGGECGGGCGGGDCGGFCG6FGBCGGGGG>DGCGGBEGG>4E7?GFGG<GGGGEG;,GBADD8ADG>2EF\n+@EAS20_8_6_100_993_1119/2 trim=60\n+TGGTTGTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCC\n++\n+B>BBB=F:FGFHFBHHHHHHHDHDGHEH=HHHHGE>8DC=\n+@EAS20_8_6_100_1153_966/2\n+TCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACATGTTTTATTTGGGCAAATTCCTGATCGA\n++\n+HHGHHHHHHGHHHHHGHHHHHHHHHHGHHHHHHHHHGHGHHHHH;HFDEHFDHDHHHHHGDHHHHDGHFGBGHHCGGHFH>ECGGHGECFFDFFD?DDDB\n+@EAS20_8_6_100_1183_226/2 correct trim=40\n+AATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCAC\n++\n+DDBBD@EEEGDHHEHBCBB0=GCGC4?.6=D8CF89:DFBGG5==*83<#?/:;+E@ABB\n+@EAS20_8_6_100_1263_900/2\n+AAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGCCACCAGGTGGTTGGTGATTTTG\n++\n+HHHEHHHEGIHHHGHGGHHHHHHHHHHHHHH=HFHHHHHFHHHGEHHFHHHGEBHHHBCHHDEGHGGF@G@HGEE=F;C9H39H=FEHFHHEFH?=AEFE\n+@EAS20_8_6_100_1277_357/2 trim=5\n+GCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGG\n++\n+FFFHFHHHHHHHHGHHDHHBBHHHHHHEEEH<GHGH@FHHHHGGHGHHHFGHHGGHGGHHHFBEFFEHHHECGIIFHEGEEDFEEH//EBD4=EF\n+@EAS20_8_6_100_1337_252/2 correct\n+CATAATGGCGATCGACATTTTCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACATGTTTT\n++\n+HHHHBHEECG=FEEFH.HHH=GEGE@HEF<BFHHBHHAHHBBBB>DGHH8HDF/=F=FF==;/FFCGGHDGBHG-B<@BFE=:FE5=E98E=E-H=@C#C\n+@EAS20_8_6_100_1432_436/2\n+CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC\n++\n+HHHHHFHHGHHHHHGGHHHHGHHHHHHHHGHHHGHHHGGGEEEHHHHHHFHEDGGGHHFHHHDGHBFGFF>BHH8FBF0F@>DFGHHBBEH>FBD@DHEG\n+@EAS20_8_6_100_1457_1209/2 correct trim=11\n+GCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGG\n++\n+HHHHBGHHHFH?HHHHCCFDB=?D=HHEEAEFEHGEB=HHC68C5??B==B=F<;C7=ECH=HE:?CE>@?<EB1.-87<<#3C9@>??\n+@EAS20_8_6_100_1609_245/2 correct trim=16\n+TCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTT\n++\n+HHEHHHGHHGHHHHDIHHHHHHHHHFHAFHFHHEIFDHFH8HHHFHHHGHHHEEB<8FFFCG>FE==9D9#0:?45/<#;B8=D\n+@EAS20_8_6_100_1637_1332/2\n+ATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTT\n++\n+HHGEHGHHHHGHIGHAHEHEHEIHGGHHHHHHHGGHHHHFHEGDGCCCHHHGHHDHHIHFEEHHHHHGHIHHHFHHIEIHHHHFAEEEHHIEHDHFFHFH\n' |
| b |
| diff -r 000000000000 -r e93c1a0678cd test-data/reference_1K.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference_1K.fa Tue Aug 09 10:46:28 2016 -0400 |
| b |
| @@ -0,0 +1,18 @@ +>NODE_1_length_1000_cov_140.62 +AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC +TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG +TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC +ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT +AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG +CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT +ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC +AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG +GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA +CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG +CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT +AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA +ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC +GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT +GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA +GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC +TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATT |
| b |
| diff -r 000000000000 -r e93c1a0678cd tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Aug 09 10:46:28 2016 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="spades" version="3.9.0"> + <repository changeset_revision="d8c8c3dc8f9a" name="package_spades_3_9_0" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |