| Previous changeset 14:09b53c1d4ab1 (2021-06-25) Next changeset 16:6b1e195506a3 (2021-10-08) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 166f7df2fa4bbcdb5c4c66a55185d5d595902ac9" |
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modified:
macros.xml minimap2.xml test-data/minimap2-self-homology.bam test-data/minimap2-test-kmer_ocurrence.bam test-data/minimap2-test-mask_len.bam test-data/minimap2-test1-fasta.bam test-data/minimap2-test1-fasta.cram test-data/minimap2-test1.bam test-data/minimap2-test2.bam test-data/minimap2-test_hifi-fasta.bam test-data/pacbio_hifi_assembly.fa |
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added:
test-data/minimap2-test_hifi-2-fasta.bam |
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| diff -r 09b53c1d4ab1 -r 7db8d4bc1eea macros.xml --- a/macros.xml Fri Jun 25 17:45:36 2021 +0000 +++ b/macros.xml Fri Oct 08 09:48:01 2021 +0000 |
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| @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">2.20</token> - <token name="@GALAXY_TOOL_VERSION@">galaxy2</token> + <token name="@TOOL_VERSION@">2.22</token> + <token name="@SUFFIX_VERSION@">0</token> <xml name="edam_ontology"> <edam_topics> <edam_topic>topic_0102</edam_topic> |
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| diff -r 09b53c1d4ab1 -r 7db8d4bc1eea minimap2.xml --- a/minimap2.xml Fri Jun 25 17:45:36 2021 +0000 +++ b/minimap2.xml Fri Oct 08 09:48:01 2021 +0000 |
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| @@ -1,6 +1,9 @@ <?xml version="1.0"?> -<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01"> +<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description> + <xrefs> + <xref type="bio.tools">minimap2</xref> + </xrefs> <macros> <import>macros.xml</import> </macros> @@ -384,7 +387,7 @@ </conditional> </actions> <change_format> - <when input="io_options.output_format" value="paf" format="tabular" /> + <when input="io_options.output_format" value="paf" format="paf" /> <when input="io_options.output_format" value="CRAM" format="cram" /> </change_format> </data> @@ -485,7 +488,7 @@ <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" /> <param name="analysis_type_selector" value="ava-ont"/> <param name="output_format" value="paf"/> - <output name="alignment_output" ftype="tabular" file="mini_reads.paf" /> + <output name="alignment_output" ftype="paf" file="mini_reads.paf" /> </test> <test> <!-- test self-homology mode --> @@ -518,6 +521,15 @@ <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="4" /> </test> <test> + <!-- test map-hifi uncompressed reference--> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa"/> + <param name="fastq_input_selector" value="single"/> + <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/> + <param name="analysis_type_selector" value="map-hifi"/> + <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-2-fasta.bam" lines_diff="4" /> + </test> + <test> <!-- test kmer ocurrence interval option --> <param name="reference_source_selector" value="history" /> <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
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| diff -r 09b53c1d4ab1 -r 7db8d4bc1eea test-data/minimap2-self-homology.bam |
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| Binary file test-data/minimap2-self-homology.bam has changed |
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| diff -r 09b53c1d4ab1 -r 7db8d4bc1eea test-data/minimap2-test-kmer_ocurrence.bam |
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| Binary file test-data/minimap2-test-kmer_ocurrence.bam has changed |
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| diff -r 09b53c1d4ab1 -r 7db8d4bc1eea test-data/minimap2-test-mask_len.bam |
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| Binary file test-data/minimap2-test-mask_len.bam has changed |
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| diff -r 09b53c1d4ab1 -r 7db8d4bc1eea test-data/minimap2-test1-fasta.bam |
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| Binary file test-data/minimap2-test1-fasta.bam has changed |
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| diff -r 09b53c1d4ab1 -r 7db8d4bc1eea test-data/minimap2-test1-fasta.cram |
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| Binary file test-data/minimap2-test1-fasta.cram has changed |
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| diff -r 09b53c1d4ab1 -r 7db8d4bc1eea test-data/minimap2-test1.bam |
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| Binary file test-data/minimap2-test1.bam has changed |
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| diff -r 09b53c1d4ab1 -r 7db8d4bc1eea test-data/minimap2-test2.bam |
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| Binary file test-data/minimap2-test2.bam has changed |
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| diff -r 09b53c1d4ab1 -r 7db8d4bc1eea test-data/minimap2-test_hifi-2-fasta.bam |
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| Binary file test-data/minimap2-test_hifi-2-fasta.bam has changed |
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| diff -r 09b53c1d4ab1 -r 7db8d4bc1eea test-data/minimap2-test_hifi-fasta.bam |
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| Binary file test-data/minimap2-test_hifi-fasta.bam has changed |
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| diff -r 09b53c1d4ab1 -r 7db8d4bc1eea test-data/pacbio_hifi_assembly.fa --- a/test-data/pacbio_hifi_assembly.fa Fri Jun 25 17:45:36 2021 +0000 +++ b/test-data/pacbio_hifi_assembly.fa Fri Oct 08 09:48:01 2021 +0000 |
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| b'@@ -8308,8884 +8308,4 @@\n TCTCGAGCAAAATCAGTATCTCCGTGACATTATATCCGGCTTTGACCAGTGCAGTCATAC\n ACATAAACTGGCTCTTAACCGCATCTCTGATTTGGAAACCTTCCAATCTAATAAAAAATT\n CGTTGCTACTCAGAGCCTGTACGATGAGCTGGTAGGTAAGGGGTCCAGTCCTGTGTGTGA\n-CACGCCAGCGATTATTGATCTGACTGGTGATGACACCAACAACCAACCTCTCTCTATTAA\n-AAGCCATAAAAAATAAAAAAGTGTTTAAAACTTAAAACTATTATAAAAAAAAACTAAGAA\n-GGCTCTTCAGACATAAAATTATTTTAAAACAAATATTAGTCTTAGAAAAGAGAGATTACA\n-ATTATTAAATGAATTTGATTATTGTACAAACAGAATGGAGTACAACAAGTCTAGGTATGA\n-TGACACACAGCAACTGCGGAATGAATTATTAGTTAGGGAGGTTGCTATAAAATATATTTT\n-CAGTAAATATGAAGTGGCTTAAGTACAACTTTGTGAGCTTATGCAGGAAGCCAGTGAGCT\n-GATGGCCTTGGTGAGATATAATGCGGAAAGATAAGAATCTCTGACTAACATCCTGCCGTG\n-TAGCTGTGACCCCTTGGTGTCTGCTCCTGAACTTGAGCAAGCAAAACCTAAACTATCCTC\n-TCCTAATAAGACACACTCTCTTGAGACATTAATTTTTTCTGACCAAATTGGGGTACGATT\n-TGGCTCAATTATACATAATAAACTTAGGTATAAGGTAACTAACTTTAGCTACAGTAACTT\n-AGGGTAAGTTAGTTATATTAAGCTTTTAATAAACAAGATTTCTCAGACAGAGGTAGATAT\n-TAATAGTACGGTTGCTTTGTTATTAGGCAACAGCCTTGACATCCAAAAAAGAGACCTAGC\n-TGATGGTGTTGAACCTGAAACCTTACTAAAATTAGGACTAAAAAAATTGATTTTGTGTGC\n-CCTGAGATACTGACAGATGGTCAGAGTACTGACCATCTGTCAGTAAAACATAACAACTTT\n-ATTCATTACTTGAATAATTATATGTACATGTTGTCATGTCAGTATGACAATATATTATTA\n-TTTGATACTAATAAATTTATTAGTGGCTTTAAGCTGACACAGAAAGCTATGTTCCTTCCT\n-AAGAAATGTAAATATATGATTGCTACATTGTTAGCTTATAATATTAACTCCATCATAGAA\n-AATATAACAAAGAATAGTTTAAGAGACGAAACAGTATTATACTGTGTCCTTCGTTCTCGA\n-TATAAACTATATTAGCAGCTCTCTCGAGTCGCTTGGCAACCGCGCGTCATTTAGCCAATT\n-GAAAAGTCAACGCCGCCTCTATGGTATCTGTGGACATAACCTCTGCAAGCATTCTTTTGA\n-AAGCGCGGCAGCCGACGCTTTGTAATAAAGTTTTTGGTCGACATTTAATTTAATAACTTG\n-TTATGGCACTTAAATTATATAACAAAAAGGTTGTAATATACTCAAGTGACCTTGTGAAAT\n-AAATTTAAAACATCGTATAGGCAAATTTAGAAAAGTTTACGTCCTGGCAAAGAAGTACAT\n-TCTAAAAAGATCAACCGATAGTTGTTTATTTGTGGTGTTTTTCAGCTTAACTTGTTTATT\n-TATATAATATCTAATATTTGGAGACGTGAGTTTCGTCATATTAAAATTTGGGAAAGCTTC\n-GTCGTCCGAAAAGTAAACTTATGAAGTCTACGTCCCTATTCGTGTACAAACAGTTTAACA\n-CGAAATATACCTGAAAACGATTATTAACCGTCTATAAATTGGCAATGTTATACCTCCAAT\n-AAGAGAAATTAGGGGGACGTTCATCGATTATGATGATTGTTCAGGATCGATGGCATTTTA\n-AGGACACGGGTGATGTACGAGATACATCGACGTGGTCCGCAAGACTTGACGATAATTCAA\n-GGACACGAGTGGTATACGAGATACATCGGCGTGATCCGCAAGACTTGGGGCCCATACGAG\n-ATATGTGCTGAAGGTCATACTACTCATAGGTTTCATCCATGAGGTGTTCCTGTGCAGTTC\n-ACATTTCTACAATGGTAAGAATCAAAAATGTTACCTAAAATACATACCTTAAACATGCCT\n-AAAACAGTAAATACAAAGGCTATTGCTAACTATAAGCAATTTGTCATATTATATCTCCAA\n-AAGGAGACTTACTGAAAGGGTAATTAAAGTGACATTGTTTATGTATAACAATACATTATT\n-AATAACAAAAGTCACTCCTTTGCAGAAACATAGTGTTTTTATTGATTTCATTGTTAGACA\n-TACTTGTATAATAATACTGAAATAGCCCAAACTGGAGCTTATTACACAAAGAATTGTGCA\n-AAATTATGAGTACTTGTATTAAAAAAGTTAAATCCAGCAATACTTATTCCTGAACAGGGT\n-TTATAACCAAATAAGCCAAAGTAATATACTAATGGCAATGCCTGTTGTAACTGACAAGCA\n-ACAGGACTGTGGATACATTCACATGCAGGCAGGTTGTGGGATAATTTGTGTTATGCACAA\n-AGATACTTAAAAGATAATATAAAATACCTGGTCTATCCAGTTAACATAGAACTAATAATT\n-ATCTATCAATATTATCAACCTAGACTCCTTGCAGGGTAGCCAGAAAAGATTAATCCTAAC\n-AATACAGTCATGAAACCTTTATTGAGATAAGAACCTTTAAGGTCAGCAGTATATATTTTG\n-CATAAAAGGAGTGTTAATATAGTGGATTATCAATATGGAATTATTAACTAGCTAGTCATA\n-GCCAGTAGTTAAAATTTCATAAAACGACCACCGTTGTAACCAATATAGAACAACAATCCT\n-CATCCTGGGTATGGAAATATTAAGTCACACTGTACCTATCAGTTCACCAAAAACAACATC\n-ACGTTGGACATTGGAAATCTCCTACCAAAGAAAGTGAGGTACAAAAAGCATGATAGGCAT\n-TTTACACAAGGACTTGCTTTTTAAGTTGCTGAAAAATTCAGAAAAACTATCAGGAATACA\n-ACATGGGTTTTACAAAGAAGCCATAATATTGGAGGCTAAAGGTATTCACTGACGGTGGTA\n-TGTATCTATGACACTAATAATGCCTTCAACGACAAACATAATTTTATTGGTTTTTGTGCA\n-AGTACTTGCACTTCAGACAAGTGAATCTTGTCCTACATATGTTTAACATTATGTATAGAA\n-ACATTATTATTAGAAACACTATTGTTTAATAATTTGAAATATAATTTATAGCTATTTTTA\n-TTAAAAATAAAAATAAAAACTTAATGCTAACACGTTAGACCTTACAGTCATAATAAATAT\n-CATCATTTCAGCCTATACTTGTCCACTGCTGAACATAGGCCTCCCCAATCGCTTTCCAGC\n-GTAACCGGTCCGATGCCACCTGCATCCAACGATTTCCTGCGATTTTCACAAGATCGTCGG\n-TCCATCTGGCAGGCGGTCGTCCTACGCTGCGCTTGCCAATACGTGGTCTCCACTCTAGAA\n-TCTTTCTGCCCCAACGCCCGTCCAATCTTCGCGCTATGTGGCCAGCCCATTGCCACTTCA\n-GCATGCTAATCCTGAGGGCTATGTCGGTGACCTTGGTTCTTCTACGAATCTCCTCATTCC\n-TGATTCGATCACGTAGAGAAACGCCGAGCATAGCTCTTTCCATAGCTCGCTGAGCAACTT\n-TGAGCTTTTTTATGAGACCTATTGTAAGAGACCACGTCTCTGATCCATATGTCATCACTG\n-GTAACACACATTGACTAAAAACTTTAGTCTTTAGGCACTGAGGTATTTTGGATGAGAAGA\n-TGTTGCGCAGTTTCCCGAACGCTGCCCAGCCGAGTTGGATTCGTCGATTGACCTCTCTCT\n-CAAAG'..b'GTGATTCGCTTTTAATTAAAATAACTTGTGAGTTATCATCTTTCCT\n-TAAGTAAACTCGGCCATACGCAGTCCAACAATATTTGTATCTCTTGGTTTTCACTAGATT\n-ACGTGCTAGAAAATGTAGTCGAGCAGCTTTTGCTGTAAGTTGTTCTGCTACGAATATAGG\n-TGTATACTCCAATGATTTGAAGCCCAAGTGTTTGGCACATAGTTTATTTTTCTGTTGAAT\n-ATTAAATGACTTACTTGCTTTCATAATTTTATTTTTCAGTATGGTTGAGGATGTCTCGAC\n-GACGATCGGAGTGTTTGTGACATTTTCTTTCTTCCCACGAACTGTGTAGATATCTTTAAT\n-ATCAGTGTTTTGTATTTGACAACCTACTGTATCGGTCAAACATAAAACCATATTCACAAG\n-GTCGTCCTTAGTTTCATCGAACTTTTTAGGCACATTTTTTATTTCAAAGTTGGTTTTCCG\n-ACTGTCCTGCTGCATATTTTCTATTTTGTCTTCCAGTAAAGTGATGTATTTTCTATCTTC\n-ATTAATTTTTCCTTCAAGAGAATCAATTTTTTTCTTGAATTCTTCATTTTGAGCAGATAA\n-AAATGCGATCGAGTTTTCGATATTGATGTTTGTTTGTTGTATTTCTTTAAGGGTGTCTGC\n-ATTTTTTTTTAAATTCTTTCTCTTGGGATTTCATTAACGAGGAAAACATGTTCTTCATTT\n-CATTTCTTAACTGAAACATATCAAAAGTCGCTTGGTCTACTTGTTTCTTTTTTGGGCGTG\n-AAGTAATGTAGTTCGGCGGCGTTGATATTCCTACGCAATCTCCTTCCGTATCCGAATGAG\n-ACATGTCCATCCAATATCACTTTGACAGTCTTTATAGGTATCCAGGTAGATAGGTAGTAT\n-ATCAATAATTACCCTTGTCAAATGTATTATGGAGTTATAAAAAATAAAATATGGATTAAA\n-TGCGTACCGATGATTTGTTGCGTAATCGAGTGTCCGTCGCCTTGGTAAGTACTTGTAGTC\n-TTGCACGTGCCAAACGCGAGGGAGAGCGGTCCGTGAGGGGTCCGGGAGCGGCGGCAAATG\n-CACAGGTGTCCGGGCGCCTGCGGGTGGAGGTGCGGCCGTCGGGAGCGGAGGAAATTTTTA\n-TTTACAAATTTAAATTATAAATTATTTTTGTAGTGCACTTCGCTTTGAGTCTAAATAACG\n-TGTATTAGGGTTCATTTTTTTTTACTAGTATTTTGAATATTTTTTATCAGCCGCGTACAC\n-GTCCTTACTGGACAGACGCACAGAGCGAAGGGGATACTGAAGAGAATGTTTTAAGATCTA\n-CACGATTAAGTCTGGGGAGGAAAATAACATATATGTAGCTTTGAGAAGCAGATATTGGTT\n-TGGAAATTCCCACTCAGCAAAGTTCAGAAGTCTTAGAAGTTGTCACTATTTTACCAGTAT\n-TATTAAAATCTTATTTTGCCACGAGTAAAAGAATAGAAGGTTATATAATACATATTGCTA\n-AAGAAATTATAGTAACCCGTTTGATCGTAGATAAGAATTTATTCAAAAGATCCGGATGCT\n-ATGGTCAAAAAACCTAGGGAATTGTAGTTTCACTGACATGAAAATCCTCCGCGGAGGTCT\n-CCGTCTATACCGCAGAAGACCTTTGGGATCTCAAAAATAATTCTTTACATCATTTAACGA\n-ATTCTACACAGCGTTTTACTAATTAATACTAATTCTGGTTACTTTAACATAGAACAATTT\n-TTATAGGTAACATGTGAAAACATAGATTATTAAATTCTTTTTCATTCCTCACACCTGCTA\n-TTTTTCTTGACAATGGCTGCTATAACCTCAATCATACTTGATATGAAATCGCATATCGTT\n-CAGATATCATCGTTTAGCAGAACAATCATAATTCATTTTTCACTTGAATAGCAAGTATGC\n-TTCACATCACTGAATTAGCGTGTTGTGAATCTCATCGCAACGAAATGACAGTTACAAAAT\n-GAGTTTTTAGTGTATAACTAGTATATGTCGCCATTTATATACCAATCTGTGATATACACG\n-GGCGCAAGCCATTTGTTTCGTCTGTTCACGAAACTACTTCAGATGCTTAGCACGAACAGA\n-TTGACGTTAGCGTAATGTTACTGAGTTTAAACGTTACCCTTACCACACTACAAATTTACT\n-AATGGCTGCTATCAATACTTAATCCAAGGATAAATTTGCCTATTACCAGTAAAACTTTCA\n-CATATTTTATATGGATCTGTCAAAATAGTAGTGACAGTAAGAAAATCTATCATTGAATAA\n-AATATTGAAACCGGACATAAACAAACATGAGTTTGTACGTTTTCGCGATAGCGTTACGCT\n-AACGCCAATGAATTCATGCTAACCCCTATGAGGATTTATAATATCAGCCTATACTGTCTA\n-CTGGGCAGAGGCCTTTTCTCAAAAATCGAGATGAGAGAGATTAGGTCATACTCCACCACG\n-CGGACCCAGTGCGAATTGGTGGAGGCAGATTTGGTGCCACCTGCTGTTGGAACTTATCAA\n-CCCGCCTATAAGGCTTCCAACTCGGCTTAACGATTACCACATAAAGTGTTAACCGGAACC\n-AATGGCTTAACGTGCCTTCCAAAGAACGGAGACGACCCATCTCAGGCCATCCGAGTCGAA\n-TGCTGGTAACCTAAGTGATCGGTAAATACCTCAGGGTCACACAGGACTACGAGCACCTGA\n-AGGTTTAGCACGATCATATTGATGTTAGCATAGTGCTGACGAGTTGATATGCCGTCTTTT\n-ATATTAAAATTTTGCTTACTAAAGATGAACGCACAATTTAGCGAACGCAAGGTAGACAGT\n-TAACAAACTAACGGTAGACTGAAAACATCACGATAACATCAATCTGTTCAAACTAAGCCC\n-GCAATTGGAAATAAAAAGTAAAAAAATAAGTGTTTTTAGTACTTGGGAGTAAGTATCATT\n-TATATTTTTGGTTACGACTTTTGTGGATGGAAGCGTGACTTAAACTAAAAGTGTGCTGAG\n-TTTTCAAGGGATAAGTCTGCTCGTGATATGGAATGTTTTTTAAGAAACTATTTTTACTTT\n-ATCTTTGTGTCGTGTCATGTGTCATAAAGTGAAAAAGGTAGAAGTAAAAAAATACATGAG\n-TAGAAGTATAGTGACATTTCGTATGGAGAGATGGAAAGTAATCAAAATCATCAAGGATCA\n-AGATCATCAAGGTTAAGCCACGTTCGAGTCGGTAAGTCTTGAGATGGGTCACCGCTTGTA\n-GTAATTTCATAATGTCCATTTACCGGTCTGCAGAAGGCACGCTAATGCACTAGTTCCGGT\n-AACCACTAAAGCCGTTCATAACGCTTTCTAAATTGACTTAACGTCTACGTTTAAATGTGA\n-TAGTCGTTAAACCTTGATGTCTTGCCTTGAGTCGTTGCAAACTTGCCTCCATCAATCCGC\n-ACTGGGTTTGCGTGGTATAATATCATACAGACTCTCTCATAACTCCAGGGAAAGAAAATA\n-AATTACATAAATCATTTTCTTTGCCCTGGATTTATAAGAGTGGGCTTTTGCCCAGCAGTG\n-GTACAATTAAGAGAAATTTATTACCATAGAGATATACATCTCAATATTTTGCTTATATTG\n-CGATACTTGGAGTTTCTTTCACGATAAAGTAATGTTACACCGGTTATTTGAACTTAGAAA\n-TTCTTATAAATATTTGCTCCACTATCGCTAGTAAGCACATAGCTTTGTGACAATATGCCG\n-TCTCCGCTGTTACCGCAAATTGAAAGGTTTTGTGACAACTTGAAATGTATCGACGGGATA\n-TTTCGACGTTTAATGACATGTTTTGGCAGGGT\n\\ No newline at end of file\n+CACGCCAGCGATTATT\n\\ No newline at end of file\n' |