| Previous changeset 11:f54f5baedfdd (2021-03-19) Next changeset 13:1f06dccdc5d1 (2021-06-11) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" |
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modified:
minimap2.xml test-data/mini_reads.paf test-data/minimap2-self-homology.bam test-data/minimap2-test1-fasta.bam test-data/minimap2-test1-fasta.cram test-data/minimap2-test1.bam test-data/minimap2-test2.bam |
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added:
macros.xml test-data/minimap2-test-kmer_ocurrence.bam test-data/minimap2-test-mask_len.bam test-data/minimap2-test_hifi-fasta.bam test-data/pacbio_hifi_assembly.fa test-data/pacbio_hifi_assembly.fa.gz test-data/pacbio_hifi_reads.fasta.gz |
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| diff -r f54f5baedfdd -r 037c6e54df11 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri May 28 21:09:55 2021 +0000 |
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| @@ -0,0 +1,40 @@ +<macros> + <token name="@TOOL_VERSION@">2.20</token> + <token name="@GALAXY_TOOL_VERSION@">galaxy0</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_0102</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_0292</edam_operation> + </edam_operations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">minimap2</requirement> + <requirement type="package" version="1.12">samtools</requirement> + </requirements> + </xml> + <xml name="pe_anaylsis_fixed_selector"> + <param name="analysis_type_selector" type="select" + label="Presets for PE reads alignment" + help="These are the minimap2 preset options for PE alignment of short reads. You can customize these and other settings in the indexing, mapping and alignment options sections below."> + <option value="sr">Short reads without splicing (-k21 -w11 --sr -F800 -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no) (sr)</option> + </param> + </xml> + <xml name="citations"> + <citations> + <citations> + <citation type="doi">10.1093/bioinformatics/btp324</citation> + <citation type="doi">10.1093/bioinformatics/btp698</citation> + <citation type="bibtex">@misc{1303.3997, + Author = {Heng Li}, + Title = {Minimap2: fast pairwise alignment for long nucleotide sequences}, + Year = {2017}, + Eprint = {arXiv:1708.01492}, + url = {https://arxiv.org/abs/1708.01492}, + }</citation> + </citations> + </citations> + </xml> +</macros> \ No newline at end of file |
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| diff -r f54f5baedfdd -r 037c6e54df11 minimap2.xml --- a/minimap2.xml Fri Mar 19 09:40:54 2021 +0000 +++ b/minimap2.xml Fri May 28 21:09:55 2021 +0000 |
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| b'@@ -1,20 +1,12 @@\n <?xml version="1.0"?>\n-<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy4" profile="17.01">\n+<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">\n <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>\n <macros>\n- <token name="@TOOL_VERSION@">2.17</token>\n- <xml name="pe_anaylsis_fixed_selector">\n- <param name="analysis_type_selector" type="select"\n- label="Presets for PE reads alignment"\n- help="These are the minimap2 preset options for PE alignment of short reads. You can customize these and other settings in the indexing, mapping and alignment options sections below.">\n- <option value="sr">Short reads without splicing (-k21 -w11 --sr -F800 -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no) (sr)</option>\n- </param>\n- </xml>\n+ <import>macros.xml</import>\n </macros>\n- <requirements>\n- <requirement type="package" version="@TOOL_VERSION@">minimap2</requirement>\n- <requirement type="package" version="1.9">samtools</requirement>\n- </requirements>\n+ <expand macro="edam_ontology"/>\n+ <expand macro="requirements"/>\n+ <expand macro="pe_anaylsis_fixed_selector"/>\n <stdio>\n <exit_code range="1:" level="fatal" />\n <regex match="\\[ERROR\\]" source="stderr" level="fatal" />\n@@ -78,7 +70,12 @@\n #if str($mapping_options.N):\n -N $mapping_options.N\n #end if\n-\n+ #if str($mapping_options.mask_len):\n+ --mask-len $mapping_options.mask_len\n+ #end if\n+ #if str($mapping_options.kmer_ocurrence_interval.interval):\n+ -U $mapping_options.kmer_ocurrence_interval.lower_limit,$mapping_options.kmer_ocurrence_interval.upper_limit\n+ #end if\n ## Alignment options\n #if str($alignment_options.splicing.splice_mode) == \'--splice\':\n --frag=no --splice\n@@ -209,6 +206,7 @@\n help="Each profile comes with the preconfigured settings mentioned in parentheses. You can customize each profile further in the indexing, mapping and alignment options sections below. If you do not select a profile here, the tool will use the per-parameter defaults listed in the below sections unless you customize them." >\n <option value="map-pb">PacBio/Oxford Nanopore read to reference mapping (-Hk19) (map-pb)</option>\n <option value="map-ont">Oxford Nanopore read to reference mapping. Slightly more sensitive for Oxford Nanopore to reference mapping (-k15). For PacBio reads, HPC minimizers consistently leads to faster performance and more sensitive results in comparison to normal minimizers. For Oxford Nanopore data, normal minimizers are better, though not much. The effectiveness of HPC is determined by the sequencing error mode. (map-ont)</option>\n+ <option value="map-hifi">PacBio HiFi reads vs reference mapping (-k19 -w19 -U50,500 -g10k -A1 -B4 -O6,26 -E2,1 -s200 ) (map-hifi)</option>\n <option value="ava-pb">PacBio all-vs-all overlap mapping (-Hk19 -Xw5 -m100 -g10000 --max-chain-skip 25) (ava-pb)</option>\n <option value="ava-ont">Oxford Nanopore all-vs-all overlap mapping (-k15 -Xw5 -m100 -g10000 -r2000 --max-chain-skip 25). Similarly, the major difference from ava-pb is that this preset is not using HPC minimizers. (ava-ont)</option>\n <option value="asm5">Long assembly to reference mapping (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100). Typically, the alignment will not extend to regions with 5% or higher sequence divergence. Only use this preset if the average divergence is far below 5%. (asm5)</option>\n@@ -236,29 +234,42 @@\n </conditional>\n <section name="indexing_options" title="Indexing options">\n <param argumen'..b'olean" truevalue="-Y" falsevalue="" label="use soft clipping for supplementary alignments ?"/>\n+ <param argument="--eqx" type="boolean" truevalue="--eqx" falsevalue="" label="Write =/X CIGAR operators"/>\n+ <param argument="-Y" type="boolean" truevalue="-Y" falsevalue="" label="Use soft clipping for supplementary alignments ?"/>\n </section>\n </inputs>\n <outputs>\n@@ -480,6 +491,41 @@\n <param name="analysis_type_selector" value="self-homology" />\n <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="2" />\n </test>\n+ <test>\n+ <!-- test mask-len option -->\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>\n+ <param name="fastq_input_selector" value="single"/>\n+ <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>\n+ <param name="analysis_type_selector" value="sr"/>\n+ <section name="mapping_options">\n+ <param name="mask_len" value="100"/>\n+ </section>\n+ <output name="alignment_output" ftype="bam" file="minimap2-test-mask_len.bam" lines_diff="2" />\n+ </test>\n+ <test>\n+ <!-- test map-hifi -->\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa.gz"/>\n+ <param name="fastq_input_selector" value="single"/>\n+ <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/>\n+ <param name="analysis_type_selector" value="map-hifi"/>\n+ <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="2" />\n+ </test>\n+ <test>\n+ <!-- test kmer ocurrence interval option -->\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>\n+ <param name="fastq_input_selector" value="single"/>\n+ <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>\n+ <param name="analysis_type_selector" value="sr"/>\n+ <conditional name="kmer_ocurrence_interval">\n+ <param name="interval" value="enabled"/>\n+ <param name="lower_limit" value="10"/>\n+ <param name="upper_limit" value="30"/>\n+ </conditional>\n+ <output name="alignment_output" ftype="bam" file="minimap2-test-kmer_ocurrence.bam" lines_diff="2" />\n+ </test>\n </tests>\n <help>\n \n@@ -546,7 +592,6 @@\n Map long mRNA/cDNA reads\n ^^^^^^^^^^^^^^^^^^^^^^^^\n \n-\n There are different long-read RNA-seq technologies, including\n tranditional full-length cDNA, EST, PacBio Iso-seq, Nanopore 2D cDNA-seq\n and Direct RNA-seq. They produce data of varying quality and properties.\n@@ -581,7 +626,6 @@\n Map short accurate genomic reads\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n \n-\n When two read files are specified, minimap2 reads from each file in turn\n and merge them into an interleaved stream internally. Two reads are\n considered to be paired if they are adjacent in the input stream and\n@@ -711,15 +755,5 @@\n should not be a big concern because even the optimal alignment may be\n wrong in such regions.\n </help>\n- <citations>\n- <citation type="doi">10.1093/bioinformatics/btp324</citation>\n- <citation type="doi">10.1093/bioinformatics/btp698</citation>\n- <citation type="bibtex">@misc{1303.3997,\n- Author = {Heng Li},\n- Title = {Minimap2: fast pairwise alignment for long nucleotide sequences},\n- Year = {2017},\n- Eprint = {arXiv:1708.01492},\n- url = {https://arxiv.org/abs/1708.01492},\n- }</citation>\n- </citations>\n+ <expand macro="citations"/>\n </tool>\n' |
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| diff -r f54f5baedfdd -r 037c6e54df11 test-data/mini_reads.paf --- a/test-data/mini_reads.paf Fri Mar 19 09:40:54 2021 +0000 +++ b/test-data/mini_reads.paf Fri May 28 21:09:55 2021 +0000 |
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| @@ -1,2 +1,2 @@ -m140213_230323_42129_c100520410120000001823082509281362_s1_X0/1263/0_8655 8655 755 8475 + m140213_230323_42129_c100520410120000001823082509281362_s1_X0/817/0_20440 20440 5798 13009 395 7727 0 tp:A:S cm:i:43 s1:i:294 dv:f:0.2746 rl:i:0 -m140213_230323_42129_c100520410120000001823082509281362_s1_X0/1447/0_15191 15191 12916 14825 - m140213_230323_42129_c100520410120000001823082509281362_s1_X0/1447/15237_17783 2546 347 2303 152 1985 0 tp:A:S cm:i:15 s1:i:133 dv:f:0.2503 rl:i:0 +m140213_230323_42129_c100520410120000001823082509281362_s1_X0/1263/0_8655 8655 755 8475 + m140213_230323_42129_c100520410120000001823082509281362_s1_X0/817/0_20440 20440 5798 13009 395 7727 0 tp:A:S cm:i:43 s1:i:296 dv:f:0.2401 rl:i:0 +m140213_230323_42129_c100520410120000001823082509281362_s1_X0/1447/0_15191 15191 12916 14825 - m140213_230323_42129_c100520410120000001823082509281362_s1_X0/1447/15237_17783 2546 347 2303 152 1985 0 tp:A:S cm:i:15 s1:i:129 dv:f:0.2215 rl:i:0 |
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| diff -r f54f5baedfdd -r 037c6e54df11 test-data/minimap2-self-homology.bam |
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| diff -r f54f5baedfdd -r 037c6e54df11 test-data/pacbio_hifi_assembly.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pacbio_hifi_assembly.fa Fri May 28 21:09:55 2021 +0000 |
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| b'@@ -0,0 +1,17191 @@\n+>tig00000044_1\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTACCTA\n+ACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACTAACCTAA\n+CCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAA\n+CTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC\n+CTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC\n+CTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC\n+CTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC\n+CTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC\n+CTAACCTAACCTAACCTAACCTAACCTAACAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+ACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTA\n+ACCTAACCCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCAACCTAACCTAACCTAACCTAACTAACCTAA\n+CCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACTAACCTAACCTAAC\n+CTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC\n+CTAACCTAACTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTA\n+ACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTA\n+ACCTAACCTAACCTAACCTAACTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAA\n+CCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACTAACCTAAC\n+CTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC\n+CTACCTAACCTAACCTAACCTAAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC\n+CTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC\n+CTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC\n+CTACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACC\n+TAACCTACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACTTAACCTAACCTAACCTAACCTAACCTAACACCTAACCTAAC\n+CTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC\n+CTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC\n+CTAACCTAACCTACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACC\n+TAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACC\n+TAACCTAACCTAACCTAACCTAACCTAACCTAAACCTAACCTAACCTAACCTAACCTAAC\n+CTAACCAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACTAACCTAACCTAACCT\n+AACCTAACCTAACCTACCTAACCTAACCTAACTAACCTAACCTAACCTAACCTAACCTAA\n+CCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAA\n+CCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACTAACCTAACCTAAC\n+CTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC\n+CTAACCTAACCTAACCTAAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAA\n+CCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAA\n+CCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACAACCTAACC\n+TAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCAAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTACCTAACCTAACCTAACCTAACCTA\n+ACCTAACCTAACCTAACCTAACTACCTAACCTAACCTAACTAACCTAACCTAACCTAACC\n+TAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACC\n+TAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACC\n+TAACCTAACCTAACCTAACCTAACTAACCTAACCTAACCTACCTAACCTAACCTAACCTA\n+ACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT\n+AACCTAACCTAACCTAACCTAACCTACCTAACCTAACCTAACCTAACCTAACCTAA'..b'ACCTGTGGTATATAGTCAATTCTCATTACA\n+AAGACATTGAAGTTGTGATTCGCTTTTAATTAAAATAACTTGTGAGTTATCATCTTTCCT\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' |
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| diff -r f54f5baedfdd -r 037c6e54df11 test-data/pacbio_hifi_reads.fasta.gz |
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