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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" |
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modified:
metaspades.xml |
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macros.xml test-data/A_R1.fastq.gz test-data/A_R2.fastq.gz test-data/B_R1.fastq.gz test-data/B_R2.fastq.gz test-data/corona_scaffold.fasta test-data/covid.fastq.gz test-data/ecoli_1K.fasta.gz test-data/ecoli_1K.fastq.gz test-data/ecoli_1K_1.fasta.gz test-data/ecoli_1K_1.fastq.gz test-data/ecoli_1K_2.fasta.gz test-data/ecoli_1K_2.fastq.gz test-data/pl1.fq.gz test-data/pl2.fq.gz |
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removed:
README.md test-data/ecoli_1K_1.fq test-data/ecoli_1K_1.fq.gz test-data/ecoli_1K_2.fq test-data/ecoli_1K_2.fq.gz test-data/reference_1K.fa |
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| diff -r 3ca2d2a9068c -r a9b8c9e204ee README.md --- a/README.md Thu Sep 16 15:25:29 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,17 +0,0 @@ -**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. |
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| diff -r 3ca2d2a9068c -r a9b8c9e204ee macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Jan 23 21:33:56 2022 +0000 |
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| b'@@ -0,0 +1,749 @@\n+<macros>\n+ <token name="@TOOL_VERSION@">3.15.3</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">spades</requirement>\n+ <requirement type="package" version="3.0">zip</requirement>\n+ <yield/>\n+ </requirements>\n+ </xml>\n+ <xml name="stdio">\n+ <stdio>\n+ <exit_code range="1:"/>\n+ <regex match="Cannot allocate memory"\n+ source="stdout"\n+ level="fatal_oom"\n+ description="Out of memory error occurred"/>\n+ <regex match="The reads contain too many k-mers to fit into available memory"\n+ source="stdout"\n+ level="fatal_oom"\n+ description="Out of memory error occurred"/>\n+ </stdio>\n+ </xml>\n+ <xml name="version_command">\n+ <version_command><![CDATA[spades.py --version 2>&1 | awk -F \'v\' \'{print $2}\']]></version_command>\n+ </xml>\n+ <token name="@INTYPES@">\n+ \n+ </token>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btv688</citation>\n+ <citation type="doi">10.1093/bioinformatics/btu266</citation>\n+ <citation type="doi">10.1093/bioinformatics/btv337</citation>\n+ <yield/>\n+ </citations>\n+ </xml>\n+ <xml name="operation_mode" token_help="">\n+ <param name="operation_mode" type="select" label="Operation mode" help="@HELP@">\n+ <option value="">Assembly and error correction</option>\n+ <option value="--only-assembler">Only assembler (--only-assembler)</option>\n+ <option value="--only-error-correction">Only error correction (--only-error-correction)</option>\n+ </param>\n+ </xml>\n+ \n+\n+<!-- PREPARE INPUT FILES-->\n+\n+<token name="@PREPROCESS_INPUT_FILES_MAIN@"><![CDATA[\n+#if $singlePaired.sPaired == "single" or $singlePaired.sPaired == "paired_interlaced"\n+ mkdir -p reads1 &&\n+ #set file_paths1 = []\n+ #for $input_file in $singlePaired.input1\n+ #set $ext = $input_file.ext.replace(\'fastqsanger\', \'fastq\')\n+ #set $fname = $input_file.element_identifier.replace(" ","_") + \'.\' + $ext\n+ #set $file_path = \'reads1/\' + $fname\n+ ln -s \'$input_file\' $file_path &&\n+ $file_paths1.append($file_path)\n+ #end for\n+#else if $singlePaired.sPaired == "paired"\n+ mkdir -p paired_reads1 &&\n+ #set fw_reads1 = []\n+ #for $input_file in $singlePaired.input1\n+ #set $ext = $input_file.ext.replace(\'fastqsanger\', \'fastq\')\n+ #set $fname = $input_file.element_identifier.replace(" ","_") + \'.\' + $ext\n+ #set $file_path = \'paired_reads1/\' + str($fname)\n+ ln -s \'$input_file\' $file_path &&\n+ $fw_reads1.append($file_path)\n+ #end for\n+ #set rv_reads1 = []\n+ #for $input_file in $singlePaired.input2\n+ #set $ext = $input_file.ext.replace(\'fastqsanger\', \'fastq\')\n+ #set $fname = $input_file.element_identifier.replace(" ","_") + \'.\' + $ext\n+ #set $file_path = \'paired_reads1/\' + str($fname)\n+ ln -s \'$input_file\' $file_path &&\n+ $rv_reads1.append($file_path)\n+ #end for\n+ #silent $fw_reads1.sort()\n+ #silent $rv_reads1.sort()\n+#else\n+ mkdir -p paired_reads1 &&\n+ #set fw_reads1 = []\n+ #set rv_reads1 = []\n+ #for $i, $input_file in enumerate($singlePaired.input)\n+ #set $ext = $input_file.forward.ext.replace(\'fastqsanger\', \'fastq\')\n+ #set $file_path = \'paired_reads1/fw\' + str($i) + \'.\' + $ext\n+ ln -s \'$input_file.forward\' $file_path &&\n+ $fw_reads1.append($file_path)\n+ #set $file_path = \'paired_reads1/rv\' + str($i) + \'.\' + $ext\n+ ln -s \'$input_file.reverse\' $file_path &&\n+ $rv_reads1.append($file_path)\n+ #end for\n+#end if\n+]]></token>\n+\n+<token name="@PREPROCESS_INPUT_FILES_ADDITIONAL@"><![CDATA[\n+#if $addition'..b'</filter>\n+ </data>\n+ </xml>\n+ <!--\n+ help\n+ -->\n+\n+ <token name="@HELP_IN@"><![CDATA[\n+\n+SPAdes takes as input paired-end reads, mate-pairs and single (unpaired) reads in FASTA and FASTQ. For IonTorrent data SPAdes also supports unpaired reads in unmapped BAM format (like the one produced by Torrent Server). However, in order to run read error correction, reads should be in FASTQ or BAM format. Sanger, Oxford Nanopore and PacBio CLR reads can be provided in both formats since SPAdes does not run error correction for these types of data.\n+\n+To run SPAdes 3.15.3 you need at least one library of the following types:\n+\n+- Illumina paired-end/high-quality mate-pairs/unpaired reads\n+- IonTorrent paired-end/high-quality mate-pairs/unpaired reads\n+- PacBio CCS reads\n+- Illumina and IonTorrent libraries should not be assembled together. All other types of input data are compatible. SPAdes should not be used if only PacBio CLR, Oxford Nanopore, Sanger reads or additional contigs are available.\n+\n+SPAdes supports mate-pair only assembly. However, we recommend to use only high-quality mate-pair libraries in this case (e.g. that do not have a paired-end part). We tested mate-pair only pipeline using Illumina Nextera mate-pairs. \n+\n+Notes:\n+\n+- It is strongly suggested to provide multiple paired-end and mate-pair libraries according to their insert size (from smallest to longest).\n+- It is not recommended to run SPAdes on PacBio reads with low coverage (less than 5).\n+- We suggest not to run SPAdes on PacBio reads for large genomes.\n+- SPAdes accepts gzip-compressed files.\n+\n+A detailed description can be found in the `input section <https://github.com/ablab/spades/#sec3.1>`_ of the manual.\n+ ]]></token>\n+ <token name="@HELP_OUT_AG@">\n+- Assembly graph\n+ </token>\n+ <token name="@HELP_OUT_AGS@">\n+- Assembly graph with scaffolds\n+ </token>\n+ <token name="@HELP_OUT_C@">\n+- Contigs\n+ </token>\n+ <token name="@HELP_OUT_CP@">\n+- Contigs paths in the assembly graph\n+ </token>\n+ <token name="@HELP_OUT_CS@">\n+- Contigs stats\n+ </token>\n+ <token name="@HELP_OUT_CR@"> \n+- Corrected reads by BayesHammer\n+ </token>\n+ <token name="@HELP_OUT_L@">\n+- Log file\n+ </token>\n+ <token name="@HELP_OUT_S@">\n+- Scaffolds (recommended for use as resulting sequences)\n+ </token>\n+ <token name="@HELP_OUT_SP@">\n+- Scaffolds paths in the assembly graph\n+ </token>\n+ <token name="@HELP_OUT_SS@">\n+- Scaffolds stats\n+ </token>\n+ <token name="@HELP_WID@">\n+SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.\n+ </token>\n+ <token name="@IONTORRENT@"><![CDATA[\n+The selection of k-mer length is non-trivial for IonTorrent. If the dataset is more or less conventional (good coverage, not high GC, etc), then use our `recommendation for long reads <https://cab.spbu.ru/files/release3.12.0/manual.html#sec3.4>`_ (e.g. assemble using k-mer lengths 21,33,55,77,99,127). However, due to increased error rate some changes of k-mer lengths (e.g. selection of shorter ones) may be required. For example, if you ran SPAdes with k-mer lengths 21,33,55,77 and then decided to assemble the same data set using more iterations and larger values of K, you can run SPAdes once again specifying the same output folder and the following options: --restart-from k77 -k 21,33,55,77,99,127 --mismatch-correction -o <previous_output_dir>. Do not forget to copy contigs and scaffolds from the previous run. We\'re planning to tackle issue of selecting k-mer lengths for IonTorrent reads in next versions.\n+\n+You may need no error correction for Hi-Q enzyme at all. However, we suggest trying to assemble your data with and without error correction and select the best variant.\n+\n+For non-trivial datasets (e.g. with high GC, low or uneven coverage) we suggest to enable single-cell mode (setting --sc option) and use k-mer lengths of 21,33,55.\n+\n+ ]]></token> \n+\n+</macros>\n' |
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| diff -r 3ca2d2a9068c -r a9b8c9e204ee metaspades.xml --- a/metaspades.xml Thu Sep 16 15:25:29 2021 +0000 +++ b/metaspades.xml Sun Jan 23 21:33:56 2022 +0000 |
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| b'@@ -1,116 +1,193 @@\n-<tool id="metaspades" name="metaSPAdes" version="3.9.0.1">\n- <description>assembler for metagenomics datasets</description>\n- <xrefs>\n- <xref type="bio.tools">metaspades</xref>\n- </xrefs>\n- <requirements>\n- <requirement type="package" version="3.9.0">spades</requirement>\n- </requirements>\n- <stdio>\n- <exit_code range="1:" />\n- </stdio>\n- <command>\n- <![CDATA[\n+<tool id="metaspades" name="metaSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">\n+ <description>metagenome assembler</description> \n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <expand macro="stdio"/>\n+ <expand macro="version_command"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+\n+#set $library = 1\n \n- if [ -n "\\$GALAXY_MEMORY_MB" ]; then\n- GALAXY_MEMORY_GB=\\$(( GALAXY_MEMORY_MB / 1024 ));\n- fi &&\n+@PREPROCESS_INPUT_FILES_MAIN@\n+#if $additional_reads.selector == \'true\'\n+ @PREPROCESS_INPUT_FILES_ADDITIONAL@\n+#end if\n+@PREPROCESS_NANOPORE_PACBIO_FILES@\n \n- ## 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\n- spades.py -o . --disable-gzip-output --meta $onlyassembler -t \\${GALAXY_SLOTS:-16} -m \\${GALAXY_MEMORY_GB:-250}\n- #if not $kmer_choice.auto_kmer_choice:\n- -k "$kmer_choice.kmers"\n- #end if\n- ## Sequence files\n- #set num=1\n- #if str( $lib_type ) == "paired_end":\n- #set prefix = \'pe\'\n+## run\n+metaspades.py\n+ -o \'output\'\n+ @RESOURCES@\n+ @INPUT_READS_MAIN@\n+ #if $additional_reads.selector == \'true\'\n+ @INPUT_READS_ADDITIONAL@\n #end if\n- --$prefix$num-$orientation\n- #for $file in $files\n- #if $file.file_type.type == "separate"\n- --$prefix$num-1 fastq:$file.file_type.fwd_reads\n- --$prefix$num-2 fastq:$file.file_type.rev_reads\n- #elif $file.file_type.type == "interleaved"\n- --$prefix$num-12 fastq:$file.file_type.interleaved_reads\n- #elif $file.file_type.type == "paired-collection"\n- --$prefix$num-1 fastq:$file.file_type.fastq_collection.forward\n- --$prefix$num-2 fastq:$file.file_type.fastq_collection.reverse\n- #end if\n- #end for\n- ]]>\n- </command>\n+ ## reads\n+ @NANOPORE_PACBIO@\n+ ## parameter\n+ @KMER@\n+ @PHREDOFFSET@\n+ @PIPELINE_OPTIONS@\n+ ## postprocessing\n+ @STATS@\n+ @CORRECTED@\n+ ]]></command>\n <inputs>\n- <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" />\n- <conditional name="kmer_choice">\n- <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" />\n- <when value="false">\n- <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." />\n- </when>\n- <when value="true" />\n- </conditional>\n- <param name="lib_type" type="select" label="Library type">\n- <option value="paired_end">Paired-end</option>\n- </param>\n- <param label="Orientation" name="orientation" type="select">\n- <option selected="true" value="fr"><![CDATA[-> <- (fr)]]></option>\n- <option value="rf"><![CDATA[<- -> (rf)]]></option>\n- <option value="ff"><![CDATA[-> -> (ff)]]></option>\n- </param>\n- <repeat name="files" title="Files" min="1">\n- <conditional name="file_type">\n- <param name="type" type="select" label="Sele'..b'- <param name="rev_reads" value="ecoli_1K_2.fq.gz" ftype="fastq.gz" />\n- <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />\n+ <!-- #2 single, separate, fastq, default parameters -->\n+ <test expect_num_outputs="4">\n+ <conditional name="singlePaired">\n+ <param name="sPaired" value="paired"/>\n+ <param name="input1" value="ecoli_1K_1.fastq.gz"/>\n+ <param name="input2" value="ecoli_1K_2.fastq.gz"/>\n+ </conditional>\n+ <output name="out_ag">\n+ <assert_contents>\n+ <has_n_lines n="36"/>\n+ <has_text_matching expression=">EDGE_5_length_1000_cov_140.620106\'"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_ags">\n+ <assert_contents>\n+ <has_n_lines n="2"/>\n+ <has_text_matching expression="S.+"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_cn">\n+ <assert_contents>\n+ <has_n_lines n="18"/>\n+ <has_text_matching expression=">NODE\\_1\\_length\\_1000\\_cov\\_.+"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_sc">\n+ <assert_contents>\n+ <has_n_lines n="18"/>\n+ <has_text_matching expression=">NODE\\_1\\_length\\_1000.+"/>\n+ </assert_contents>\n+ </output>\n </test>\n+ <!-- #3 only corrected reads are created as an output -->\n+ <test expect_num_outputs="2">\n+ <conditional name="singlePaired">\n+ <param name="sPaired" value="paired_interlaced"/>\n+ <param name="input1" value="ecoli_1K.fastq.gz"/>\n+ </conditional>\n+ <param name="optional_output" value="cr,l"/>\n+ <output_collection name="out_cr" type="list" count="3">\n+ <element name="ecoli_1K.fastq.gz_1.00.0_0.cor">\n+ <assert_contents>\n+ <has_size value="130317" delta="1000"/>\n+ </assert_contents>\n+ </element>\n+ <element name="ecoli_1K.fastq.gz_2.00.0_0.cor">\n+ <assert_contents>\n+ <has_size value="130317" delta="1000"/>\n+ </assert_contents>\n+ </element>\n+ <element name="ecoli_1K.fastq.gz__unpaired.00.0_0.cor">\n+ <assert_contents>\n+ <has_size value="20" delta="5"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ <output name="out_l">\n+ <assert_contents>\n+ <has_text_matching expression="Thank you for using SPAdes!"/>\n+ </assert_contents>\n+ </output>\n+ </test> \n </tests>\n- <help>\n-<![CDATA[\n+ <help><![CDATA[\n+.. class:: infomark\n+\n **What it does**\n \n-SPAdes \xe2\x80\x93 St. Petersburg genome assembler \xe2\x80\x93 is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes.\n-]]>\n- </help>\n- <citations>\n- <citation type="doi">10.1089/cmb.2012.0021</citation>\n- </citations>\n+@HELP_WID@\n+\n+metaSPAdes is a subtool for assembling metagenomic data sets.\n+\n+**Input**\n+\n+@HELP_IN@\n+\n+**Output**\n+\n+@HELP_OUT_AG@\n+@HELP_OUT_AGS@\n+@HELP_OUT_C@\n+@HELP_OUT_CP@\n+@HELP_OUT_CR@\n+@HELP_OUT_CS@\n+@HELP_OUT_L@\n+@HELP_OUT_S@\n+@HELP_OUT_SP@\n+@HELP_OUT_SS@\n+\n+**References**\n+\n+More information can be found on `github <https://github.com/ablab/spades>`_ and on the `project website <http://cab.spbu.ru/software/meta-spades>`_.\n+ ]]></help>\n+ <expand macro="citations">\n+ <citation type="doi">10.1101/gr.213959.116</citation>\n+ </expand>\n </tool>\n' |
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| diff -r 3ca2d2a9068c -r a9b8c9e204ee test-data/corona_scaffold.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/corona_scaffold.fasta Sun Jan 23 21:33:56 2022 +0000 |
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| @@ -0,0 +1,18 @@ +>NODE_1_length_1009_cluster_1_candidate_1_domains_2 +GTTCAAGCTGAGGCAAAACGCCTTTTTCAACTTCTACTAAGCCACAAGTGCCATCTTTAG +GATGTTGACGTGCCTCTGATAAGACCGCCTCCACTGGAGGATACACAGGTTTAAAGGTTT +ATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAAC +GAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATA +ATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCT +GCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGT +GACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAAC +TCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGG +AGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAG +TTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATG +CTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTC +AGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAG +TGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTT +ACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAG +ATTTAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAA +CAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCCTGGTCATGTTGAG +CTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACAC |
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| diff -r 3ca2d2a9068c -r a9b8c9e204ee test-data/ecoli_1K_1.fq --- a/test-data/ecoli_1K_1.fq Thu Sep 16 15:25:29 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,8216 +0,0 @@\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' |
| b |
| diff -r 3ca2d2a9068c -r a9b8c9e204ee test-data/ecoli_1K_1.fq.gz |
| b |
| Binary file test-data/ecoli_1K_1.fq.gz has changed |
| b |
| diff -r 3ca2d2a9068c -r a9b8c9e204ee test-data/ecoli_1K_2.fasta.gz |
| b |
| Binary file test-data/ecoli_1K_2.fasta.gz has changed |
| b |
| diff -r 3ca2d2a9068c -r a9b8c9e204ee test-data/ecoli_1K_2.fastq.gz |
| b |
| Binary file test-data/ecoli_1K_2.fastq.gz has changed |
| b |
| diff -r 3ca2d2a9068c -r a9b8c9e204ee test-data/ecoli_1K_2.fq --- a/test-data/ecoli_1K_2.fq Thu Sep 16 15:25:29 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,8216 +0,0 @@\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 3ca2d2a9068c -r a9b8c9e204ee test-data/ecoli_1K_2.fq.gz |
| b |
| Binary file test-data/ecoli_1K_2.fq.gz has changed |
| b |
| diff -r 3ca2d2a9068c -r a9b8c9e204ee test-data/pl1.fq.gz |
| b |
| Binary file test-data/pl1.fq.gz has changed |
| b |
| diff -r 3ca2d2a9068c -r a9b8c9e204ee test-data/pl2.fq.gz |
| b |
| Binary file test-data/pl2.fq.gz has changed |
| b |
| diff -r 3ca2d2a9068c -r a9b8c9e204ee test-data/reference_1K.fa --- a/test-data/reference_1K.fa Thu Sep 16 15:25:29 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,18 +0,0 @@ ->NODE_1_length_1000_cov_140.62 -AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC -TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG -TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC -ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT -AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG -CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT -ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC -AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG -GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA -CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG -CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT -AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA -ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC -GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT -GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA -GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC -TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATT |