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42 lines
1.2 KiB
YAML
42 lines
1.2 KiB
YAML
name: bwa mem
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description: Performs fastq alignment to a fasta reference using the burrows-wheeler aligner
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keywords:
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- mem
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- bwa
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- alignment
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tools:
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- bwa:
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description: |
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BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
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homepage: http://bio-bwa.sourceforge.net/
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documentation: http://www.htslib.org/doc/samtools.html
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arxiv: arXiv:1303.3997
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input:
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-
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- id:
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type: val
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description: read/read pair id
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- reads:
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type: file
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description: Input fastq file
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pattern: *.{fastq,fq}
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- index:
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type: file
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description: bwa indexes file
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pattern: *.{amb,ann,bwt,pac,sa}
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- prefix:
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type: val
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description: bwa index prefix, equivalent to index file names without extensions. Usually the reference genome file name unless otherwise specified.
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output:
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-
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- bam:
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type: file
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description: Output bam file
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pattern: *.bam
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- bamindex:
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type: file
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description: Output bam index file
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pattern: *.bai
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authors:
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- @jeremy1805
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