nf-core_modules/software/bowtie2/meta.yml

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name: Bowtie 2
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description: Ultrafast alignment to reference genome
keywords:
- Alignment
- Short reads
- FM Index
tools:
- fastqc:
description: |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
to long reference sequences. It is particularly good at aligning reads of about
50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively
long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep
its memory footprint small: for the human genome, its memory footprint is typically
around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
input:
-
- sample_id:
type: string
description: Sample identifier
- reads:
type: file
description: Input FastQ file, or pair of files
output:
-
- report:
type: file
description: mapping statistics report
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pattern: "*bowtie2_stats.txt"
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- alignment:
type: file
description: alignment file in BAM format
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pattern: "*bowtie2.bam"
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authors:
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- "@FelixKrueger"