2020-07-11 11:42:13 +00:00
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name: Bowtie 2
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2020-03-19 18:13:15 +00:00
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description: Ultrafast alignment to reference genome
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keywords:
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- Alignment
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- Short reads
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- FM Index
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tools:
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- fastqc:
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description: |
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Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
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to long reference sequences. It is particularly good at aligning reads of about
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50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively
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long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep
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its memory footprint small: for the human genome, its memory footprint is typically
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around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
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homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
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documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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input:
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-
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- sample_id:
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type: string
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description: Sample identifier
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- reads:
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type: file
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description: Input FastQ file, or pair of files
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output:
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-
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- report:
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type: file
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description: mapping statistics report
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pattern: *bowtie2_stats.txt
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- alignment:
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type: file
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description: alignment file in BAM format
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pattern: *bowtie2.bam
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authors:
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- @FelixKrueger
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