| Previous changeset 5:87c11c05d238 (2021-07-18) Next changeset 7:ce5d418183c5 (2023-06-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 168993a4e148506b1d3998c536caa2e501c36ccf |
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modified:
kallisto_pseudo.xml macros.xml test-data/kallisto_quant_out4.bam test-data/kallisto_quant_out5.bam |
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added:
test-data/annotation.gtf.gz test-data/chromosome_size.tabular test-data/kallisto_quant_out7.tab test-data/reads_forward.fastq.gz test-data/reads_reverse.fastq.gz test-data/transcripts.fasta |
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| diff -r 87c11c05d238 -r a157781cddd7 kallisto_pseudo.xml --- a/kallisto_pseudo.xml Sun Jul 18 17:53:43 2021 +0000 +++ b/kallisto_pseudo.xml Wed May 31 20:10:19 2023 +0000 |
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| @@ -1,9 +1,13 @@ <?xml version="1.0"?> <tool id="kallisto_pseudo" name="Kallisto pseudo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> - <description>- run pseudoalignment on RNA-Seq transcripts</description> + <description>run pseudoalignment on RNA-Seq transcripts</description> <macros> <import>macros.xml</import> </macros> + <xrefs> + <xref type="bio.tools">kallisto</xref> + </xrefs> + <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ @@ -67,7 +71,7 @@ </param> <when value="single"> <param name="reads" type="data" format="fastq,fastq.gz" multiple="True" label="Reads in FASTQ format" /> - <param name="fragment_length" argument="--fragment-length" type="integer" value="200" label="Average fragment length" /> + <param argument="--fragment-length" type="integer" value="200" label="Average fragment length" /> <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" /> </when> <when value="paired"> @@ -165,7 +169,7 @@ <param name="single_paired_selector" value="paired" /> <param name="collection_selector" value="datasets" /> <param name="umi" value="yes" /> - <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" /> + <param name="forward" ftype="tabular" dbkey="sacCer2" value="sacCer2_chrM.umi" /> <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" /> <output name="sample"> <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out6.tab" ftype="tabular" /> |
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| diff -r 87c11c05d238 -r a157781cddd7 macros.xml --- a/macros.xml Sun Jul 18 17:53:43 2021 +0000 +++ b/macros.xml Wed May 31 20:10:19 2023 +0000 |
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| @@ -1,11 +1,11 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">0.46.2</token> + <token name="@TOOL_VERSION@">0.48.0</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">kallisto</requirement> - <requirement type="package" version="1.12">samtools</requirement> + <requirement type="package" version="1.14">samtools</requirement> </requirements> </xml> <xml name="citations"> |
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| diff -r 87c11c05d238 -r a157781cddd7 test-data/annotation.gtf.gz |
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| Binary file test-data/annotation.gtf.gz has changed |
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| diff -r 87c11c05d238 -r a157781cddd7 test-data/chromosome_size.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chromosome_size.tabular Wed May 31 20:10:19 2023 +0000 |
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| @@ -0,0 +1,1 @@ +chr1 24999771 |
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| diff -r 87c11c05d238 -r a157781cddd7 test-data/kallisto_quant_out4.bam |
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| Binary file test-data/kallisto_quant_out4.bam has changed |
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| diff -r 87c11c05d238 -r a157781cddd7 test-data/kallisto_quant_out5.bam |
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| Binary file test-data/kallisto_quant_out5.bam has changed |
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| diff -r 87c11c05d238 -r a157781cddd7 test-data/kallisto_quant_out7.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_quant_out7.tab Wed May 31 20:10:19 2023 +0000 |
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| @@ -0,0 +1,16 @@ +target_id length eff_length est_counts tpm +NM_001168316 2283 2105.9 160.693 12587.6 +NM_174914 2385 2207.9 1500.61 112117 +NR_031764 1853 1675.9 102.695 10108.4 +NM_004503 1681 1503.9 330.216 36221.2 +NM_006897 1541 1363.9 664 80309.8 +NM_014212 2037 1859.9 55 4878.16 +NM_014620 2300 2122.9 589.807 45831.5 +NM_017409 1959 1781.9 47 4351.09 +NM_017410 2396 2218.9 42 3122.45 +NM_018953 1612 1434.9 227.994 26211.1 +NM_022658 2288 2110.9 4881 381438 +NM_153633 1666 1488.9 362.124 40121.2 +NM_153693 2072 1894.9 74.8502 6516.13 +NM_173860 849 671.903 962 236185 +NR_003084 1640 1462.9 0.00847856 0.956071 |
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| diff -r 87c11c05d238 -r a157781cddd7 test-data/reads_forward.fastq.gz |
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| Binary file test-data/reads_forward.fastq.gz has changed |
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| diff -r 87c11c05d238 -r a157781cddd7 test-data/reads_reverse.fastq.gz |
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| Binary file test-data/reads_reverse.fastq.gz has changed |
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| diff -r 87c11c05d238 -r a157781cddd7 test-data/transcripts.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts.fasta Wed May 31 20:10:19 2023 +0000 |
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| b'@@ -0,0 +1,498 @@\n+>NM_001168316\n+TTAGTGAGGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGGAAACC\n+TACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTCACTGTGGGCACCAGAGACAGGGAC\n+CCAATGTGGAGACCTGTGAGCCTGTGTCCGGCCCTGAACTCTCAAGCACAGGGCAGGCTT\n+CCTGAGCATTGAAGAGAATATGTGGGAGAACAAAACAGAAACTGAAAGAATATGCAAGGT\n+GTCTTTCTTGGATGTTATTCCATGATAGATAGTAGGGGCAGGAGTGAGAGAGGCTGACTA\n+GGTCTGGACATGGAGGCTGGAAGAGTCAGGGTGTGATTCGGAGAGGCGCATGAGAAGGAA\n+GGTGGATTTTAAGGCTGGAAATCTGAGGGTCAGTGGTCCAAGTCACTCAGAGACAGAATC\n+ACAGCATAGCCCTTGCTGATGGCAAACAAAGGAGGACAAGAGGACTGGAAAGAATTCTGC\n+TAGCAGGCAGGAGCTAGTAAGGATGAATTTGTAGCAAAATTAGCAAGTGGAAAGGATGAT\n+TTTTGGCCATTTTTCCTGTTCTTCAAGAAAACAGGAGATAACTAGAAGGACTAGAGAATG\n+GGGCTGCCAGAACTAGTGGGAAGCTCCCTAGAAATGGTGACATCGCCCACCAAACAGACC\n+CCGCCAAGGCTGCACCTGGCCTTATGTCTCCTTCACCTTTCTGGCCCCACGCAGCCACCA\n+GACAGCCATGCCCAGCAGCTTCCCACAAAGCCATAGAGTCCCCAGAGTGAGCCCCAGCAG\n+AAACACAAAAACGTCGAGCAGGTACTGCTCATGCCAGGGCTGCTGAAAGACATAGGGCTT\n+GAGGTGCGTCGCGCCCCCTGTCTGGAGGACGTGGTCAATCCAGCCCACCAGCCGCTGTGT\n+GGGGCTGAGCGGGTGGGAGCGCAGGATGACACTGGCAGCCACTGCCGCGGACTTGTATCT\n+CTTGTCTTCCATGATTTGTTTCATCTTAAGAGCCAATGTCTCTGCCTTGAGCTTCTTTAA\n+CTGAATAGAAACACCAAACTTTTTGGCTTCTACTCGGACCATGTTTTCAGGCTGGTCTCC\n+AAAGAGAGGGATCCCCACCATGGGCACACCATGCTGGATGGCCTCCATTATGCTATTCTG\n+CCCGCCGTGGGTGACAAACAGACGGATGCTTGGGTGAGCCAGGAGGTCACTCTGAGGAAG\n+CCAGTCCACAATTTTCACATTTGCAGCCAGGTGGACATCTTTGGGCCAATGAGAACACTG\n+ACACTTCCATATCACCCCTTGGGGTAGGTGAGCAAAGGCATTGTTCATCTCCTTGAAGAT\n+TTCCGGATTCTGACAGGTGTTCACCATGGAGCCCAAGGTCACAAGGACAAAACCAGAGTC\n+CCCAAACTTGGCAATGAAGTTCTCCAAGTCTTGTGGTACTGGTTTAATAGGTTTTTCCAT\n+CAAGCCTCCAACATAAACAGTGTTGGGAAGCAGAGGTCGAGCAAAATCAAAGGCAAAGTC\n+AGAGTTAATGAACCACAACTCTGCTTTCAGTAGAAGATGAGACAAAACTGGCCTAGAGCC\n+TTCTGTGAAATGTTCCTTGATGGTGTTGTCAAATGTAGACTGCATGTGCTGTTGCCTCCT\n+GCAGAAACTAAAGAACATCAGAAAATTCTTCACTCGGCCCCAGAAGTCCATGTGATCAGT\n+CAGCAAGGAACGGAATACTGGAACATAAGACAAGGGGATTGGTAGCCCAAATTCCAAAGA\n+GCCGAATGAAGTGGAAAGAATGGCCACAAATGGCTTCCCAAGCTTCTCAGCAATCAGGAA\n+AGGACAGTAGTCAAAAGTTTCAACTATCACCATGTCGAAGTTCTCATTCTTTAAGGAATC\n+CATGATATCCTTTCTATTTAAAAAATGACTGCACTGCAACGCCAAGTATTCTAGAACATT\n+TAATAAGTTTTCAAATTTTCCTCTGCCACCTAAAGTTTCTTCCAGAAAGAAATCAAAACT\n+CTTTTTAAATTCTCTTTGATGATCTTCAGGTGCAAGCCAACTGATAACTTGATATGATTT\n+TTCTTCCTTTTTAAAATCTACTGTAGATATTGTCAGGATTTTGGCAGCCTCTGAGAGCAG\n+GACCCCAGGGAGAAGGAAGCCCACTAGAAGAAGCACTCGCTGCCCAGCCATGCTCACTTC\n+TACGGAAGCCGCGGATCTCAGCCTGGGCTGCGCGCCCTGCGCCCGGCTAAGGGACCCTGT\n+GCACCTCAGTGCGCCAAAGGCACTGGCTGTGGGTAGAGGTAGGAGTAAGGATCCTGCCAG\n+TCT\n+>NM_174914\n+TTAGTGAGGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGGAAACC\n+TACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTCACTGTGGGCACCAGAGACAGGGAC\n+CCAATGTGGAGACCTGTGAGCCTGTGTCCGGCCCTGAACTCTCAAGCACAGGGCAGGCTT\n+CCTGAGCATTGAAGAGAATATGTGGGAGAACAAAACAGAAACTGAAAGAATATGCAAGGT\n+GTCTTTCTTGGATGTTATTCCATGATAGATAGTAGGGGCAGGAGTGAGAGAGGCTGACTA\n+GGTCTGGACATGGAGGCTGGAAGAGTCAGGGTGTGATTCGGAGAGGCGCATGAGAAGGAA\n+GGTGGATTTTAAGGCTGGAAATCTGAGGGTCAGTGGTCCAAGTCACTCAGAGACAGAATC\n+ACAGCATAGCCCTTGCTGATGGCAAACAAAGGAGGACAAGAGGACTGGAAAGAATTCTGC\n+TAGCAGGCAGGAGCTAGTAAGGATGAATTTGTAGCAAAATTAGCAAGTGGAAAGGATGAT\n+TTTTGGCCATTTTTCCTGTTCTTCAAGAAAACAGGAGATAACTAGAAGGACTAGAGAATG\n+GGGCTGCCAGAACTAGTGGGAAGCTCCCTAGAAATGGTGACATCGCCCACCAAACAGACC\n+CCGCCAAGGCTGCACCTGGCCTTATGTCTCCTTCACCTTTCTGGCCCCACGCAGCCACCA\n+GACAGCCATGCCCAGCAGCTTCCCACAAAGCCATAGAGTCCCCAGAGTGAGCCCCAGCAG\n+AAACACAAAAACGTCGAGCAGGTACTGCTCATGCCAGGGCTGCTGAAAGACATAGGGCTT\n+GAGGTGCGTCGCGCCCCCTGTCTGGAGGACGTGGTCAATCCAGCCCACCAGCCGCTGTGT\n+GGGGCTGAGCGGGTGGGAGCGCAGGATGACACTGGCAGCCACTGCCGCGGACTTGTATCT\n+CTTGTCTTCCATGATTTGTTTCATCTTAAGAGCCAATGTCTCTGCCTTGAGCTTCTTTAA\n+CTGAATAGAAACACCAAACTTTTTGGCTTCTACTCGGACCATGTTTTCAGGCTGGTCTCC\n+AAAGAGAGGGATCCCCACCATGGGCACACCATGCTGGATGGCCTCCATTATGCTATTCTG\n+CCCGCCGTGGGTGACAAACAGACGGATGCTTGGGTGAGCCAGGAGGTCACTCTGAGGAAG\n+CCAGTCCACAATTTTCACATTTGCAGCCAGGTGGACATCTTTGGGCCAATGAGAACACTG\n+ACACTTCCATATCACCCCTTGGGGTAGGTGAGCAAAGGCATTGTTCATCTCCTTGAAGAT\n+TTCCGGATTCTGACAGGTGTTCACCATGGAGCCCAAGGTCACAAGGACAAAACCAGAGTC\n+CCCAAACTTGGCAATGAAGTTCTCCAAGTCTTGTGGTACTGGTTTAATAGGTTTTTCCAT\n+CAAGCCTCCAACATAAACAGTGTTGGGAAGCAGAGGTCGAGCAAAATCAAAGGCAAAGTC\n+AGAGTTAATGAACCACAACTCTGCTTTCAGTAGAAGATGAGA'..b'G\n+GATCTAATTCCTTTTACCAGGAGAAAGACATGCTCTCAAACTGCAGACAAAACACCTTAG\n+GACATAACACACAGACCTCAATCGCTCAGGATTTTAGTTCTGAGCAGGGCAGGACTGCGC\n+CCCAGGACCAGAAAGCCAGTATCCAGATTTACCCCTGGATGCAGCGAATGAATTCGCACA\n+GTGGGGTCGGCTACGGAGCGGACCGGAGGCGCGGCCGCCAGATCTACTCGCGGTACCAGA\n+CCCTGGAACTGGAGAAGGAATTTCACTTCAATCGCTACCTAACGCGGCGCCGGCGCATCG\n+AGATCGCCAACGCGCTTTGCCTGACCGAGCGACAGATCAAAATCTGGTTCCAGAACCGCC\n+GGATGAAGTGGAAAAAAGAATCTAATCTCACATCCACTCTCTCGGGGGGCGGCGGAGGGG\n+CCACCGCCGACAGCCTGGGCGGAAAAGAGGAAAAGCGGGAAGAGACAGAAGAGGAGAAGC\n+AGAAAGAGTGACCAGGACTGTCCCTGCCACCCCTCTCTCCCTTTCTCCCTCGCTCCCCAC\n+CAACTCTCCCCTAATCACACACTCTGTATTTATCACTGGCACAATTGATGTGTTTTGATT\n+CCCTAAAACAAAATTAGGGAGTCAAACGTGGACCTGAAAGTCAGCTCTGGACCCCCTCCC\n+TCACCGCACAACTCTCTTTCACCACGCGCCTCCTCCTCCTCGCTCCCTTGCTAGCTCGTT\n+CTCGGCTTGTCTACAGGCCCTTTTCCCCGTCCAGGCCTTGGGGGCTCGGACCCTGAACTC\n+AGACTCTACAGATTGCCCTCCAAGTGAGGACTTGGCTCCCCCACTCCTTCGACGCCCCCA\n+CCCCCGCCCCCCGTGCAGAGAGCCGGCTCCTGGGCCTGCTGGGGCCTCTGCTCCAGGGCC\n+TCAGGGCCCGGCCTGGCAGCCGGGGAGGGCCGGAGGCCCAAGGAGGGCGCGCCTTGGCCC\n+CACACCAACCCCCAGGGCCTCCCCGCAGTCCCTGCCTAGCCCCTCTGCCCCAGCAAATGC\n+CCAGCCCAGGCAAATTGTATTTAAAGAATCCTGGGGGTCATTATGGCATTTTACAAACTG\n+TGACCGTTTCTGTGTGAAGATTTTTAGCTGTATTTGTGGTCTCTGTATTTATATTTATGT\n+TTAGCACCGTCAGTGTTCCTATCCAATTTCAAAAAAGGAAAAAAAAGAGGGAAAATTACA\n+AAAAGAGAGAAAAAAAGTGAATGACGTTTGTTTAGCCAGTAGGAGAAAATAAATAAATAA\n+ATAAATCCCTTCGTGTTACCCTCCTGTATAAATCCAACCTCTGGGTCCGTTCTCGAATAT\n+TTAATAAAACTGATATTATTTTTAAAACTTTA\n+>NM_173860\n+ATGGGCGAGCATAATCTCCTGAATCCCGGGTTTGTGGGGCCGCTGGTAAACATCCACACG\n+GGAGACACCTTCTACTTCCCCAACTTCCGCGCGTCCGGGGCGCAGCTTCCCGGGCTGCCT\n+TCGCTGTCCTACCCACGCCGCGACAACGTGTGCTCCCTGTCCTGGCCGTCGGCGGAGCCG\n+TGCAATGGCTACCCGCAGCCCTACCTCGGCAGCCCAGTGTCTCTCAACCCTCCCTTCGGC\n+CGCACGTGCGAGCTGGCGCGCGTGGAGGACGGCAAGGGTTACTACCGCGAGCCGTGCGCC\n+GAGGGTGGCGGCGGGGGCCTGAAGCGTGAGGAGCGCGGGCGCGACCCGGGAGCCGGGCCC\n+GGGGCAGCGCTGCTCCCGCTGGAGCCGTCGGGGCCGCCTGCGCTCGGCTTCAAGTACGAC\n+TACGCGGCGGGCGGCGGCGGTGGCGACGGCGGCGGCGGCGCAGGACCTCCGCACGACCCG\n+CCCTCCTGCCAGTCGCTGGAATCCGACTCCAGTTCGTCCCTGCTCAACGAGGGCAACAAG\n+GGCGCCGGCGCAGGCGACCCCGGCAGCTTGGTATCGCCGTTGAACCCCGGCGGCGGGCTC\n+TCGGCCAGCGGCGCGCCCTGGTACCCGATCAACAGCCGCTCTCGGAAGAAGCGCAAGCCC\n+TATTCGAAGTTGCAACTGGCAGAGCTGGAGGGCGAGTTTCTGGTCAACGAGTTCATCACA\n+CGCCAGCGCCGGAGGGAACTCTCAGACCGCTTGAATCTTAGTGACCAGCAGGTCAAGATC\n+TGGTTTCAGAACCGGAGAATGAAAAAGAAAAGACTTCTGTTGAGGGAGCAAGCTCTCTCC\n+TTCTTTTAA\n+>NR_003084\n+TTATTGTGGTTTGTCCGTTCCGAGCGCTCCGCAGAACAGTCCTCCCTGTAAGAGCCTAAC\n+CATTGCCAGGGAAACCTGCCCTGGGCGCTCCCTTCATTAGCAGTATTTTTTTTAAATTAA\n+TCTGATTAATAATTATTTTTCCCCCATTTAATTTTTTTTCCTCCCAGGTGGAGTTGCCGA\n+AGCTGGGGGCAGCTGGGGAGGGTGGGGATGGGAGGGGAGAGACAGAAGTTGAGGGCATCT\n+CTCTCTTCCTTCCCGACCCTCTGGCCCCCAAGGGGCAGGAGGAATGCAGGAGCAGGAGTT\n+GAGCTTGGGAGCTGCAGATGCCTCCGCCCCTCCTCTCTCCCAGGCTCTTCCTCCTGCCCC\n+CTTCTTGCAACTCTCCTTAATTTTGTTTGGCTTTTGGATGATTATAATTATTTTTATTTT\n+TGAATTTATATAAAGTATATGTGTGTGTGTGTGGAGCTGAGACAGGCTCGGCAGCGGCAC\n+AGAATGAGGGAAGACGAGAAAGAGAGTGGGAGAGAGAGAGGCAGAGAGGGAGAGAGGGAG\n+AGTGACAGCAGCGCTCGAGACGGACGGCAAGCGGTCCCGAACCAGTTACACGCGCTACCA\n+GACTCTGGAACTCGAGAAAGAATTCCACTTTAACCGCTACCTCACTCGCCGCAGGCGCAT\n+AGAGATCGCCAACAACTTGTGTCTCAATGAGAGACAGATCAAGATCTGGTTCCAGAACCG\n+CAGGATGAAGTGGAAGAAAGATTCCAAAATGAAAAGCAAAGAGGCTCTTTAGAGGCAGCG\n+GGGGAGGCCCGCAGAGCGCGCCCCTAGCCGGTTCCTGTCCCTGCGCCTTTCCTTTTCGCC\n+TTTCCTCTCTATATTTCGGGTCGGGGGCAGGTGCTGGAGCACTGGGCTCCCGGGCCCCAC\n+AGACAAAAGCGCTTTTCCTTGGCATTCCGCATCCCTACCGACCCAGGGTTCCCGCGGGGC\n+TGTCGGCGCTGCCCCATCTCCCCTCAGCTCGGCTCAGCTCGGTACCCGGGGCCCAGGGCA\n+AGCTCCGCAGGACTTCCCCGGAGGGCTGCGGCGTACAGGCTGGCGCAGAACGAACCTTGG\n+CCTGGGCCGTATCTCCGGCTCCCAGCCTCAGCGCGGCCCTCCCGAGTTAAGGTGGGCCCG\n+GCCCGCGCCACAGGACCCTCGCCGGACCCTCTAACCTCGCCCTCTCCTTTGTTCCCGGCT\n+GGACGGGTTAGACAGCCAAAGGCTGGCGAGAGTCTGGCCCTAGACTCGGGGTGCTTCCTT\n+GTAGCGACTAAACTAGATTTTCACTTATGAATGATTTGCATATGAAAGGAGAGCATCGGC\n+CTAGGGCCCCCACAGTTGCTCTATGCTTTCCAAACCTTATCTCCACAACCTCTTCCCCCC\n+AAAACCCGGGAACCTCCCCAGCCTGCGCCTGCTGCATGCCCTCTCAGGCCGGCAGCCCCA\n+GCCTGCTAGCTAGCTCAACTAGTGGGGTTTCCTGGCACTGGACCCCAGCAAGTGGTCCTA\n+GAGGCCCTTTGCTGTCCCATAGTCCCTGCCACGAATTTCTGTGCCCTCCTGACCCATTGC\n+TGTTGTCCAACTATTTATTGACTCTGGGTCCTTCCTGAAACTATATTTTGTCATATCAAA\n+TAAAGAGAGAACAGGACTAA\n' 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