bowtie.debian.yaml

identifiers:
  - biotools: bowtie
  - doi: 10.1186/gb-2009-10-3-r25
  - debian: bowtie
  - bioconda: bowtie
  - scicrunch: SCR_005476
  - omictools: OMICS_00653
homepage: http://bowtie-bio.sourceforge.net/
summary: Ultrafast memory-efficient short read aligner
description: >
  This package addresses the problem to interpret the results from the
  latest (2010) DNA sequencing technologies. Those will yield fairly
  short stretches and those cannot be interpreted directly. It is the
  challenge for tools like Bowtie to give a chromosomal location to the
  short stretches of DNA sequenced per run.
  .
  Bowtie aligns short DNA sequences (reads) to the human genome at a rate
  of over 25 million 35-bp reads per hour. Bowtie indexes the genome with
  a Burrows-Wheeler index to keep its memory footprint small: typically
  about 2.2 GB for the human genome (2.9 GB for paired-end).
version: 1.2.3
edam:
  version: unknown
  topics:
    - Genomics
  scopes:
    - name: summary
      function:
        - Genome indexing
        - Sequence alignment generation
      input:
        - data: Nucleic acid sequence (raw)
          formats:
            - FASTA
            - FASTQ
      output:
        - data: Sequence alignment (nucleic acid)
          formats:
            - SAM
    - name: bowtie-build
      function:
        - G
        - e
        - n
        - o
        - m
        - e
        -  
        - i
        - n
        - d
        - e
        - x
        - i
        - n
        - g
        -  
        - (
        - B
        - u
        - r
        - r
        - o
        - w
        - s
        - -
        - W
        - h
        - e
        - e
        - l
        - e
        - r
        - )
      input:
        - data: Nucleic acid sequence (raw)
          formats:
            - FASTA
      output:
        - data: Genome index
          formats:
            - Bowtie index format EBWT
            - Bowtie long index format EBTWL
    - name: bowtie-inspect
      function:
        - Sequence retrieval
        - Metadata retrieval
        - Data index analysis
      input:
        - data: Genome index
          formats:
            - Bowtie index format EBWT
            - Bowtie long index format EBTWL
      output:
        - data: Nucleic acid sequence (raw)
          formats:
            - FASTA
            - plain text format (unformatted)
    - name: bowtie
      function:
        - Sequence database search (by sequence using word-based methods)
        - Sequence alignment generation
      input:
        - data: Genome index
        - data: Nucleic acid sequence (raw)
          formats:
            - plain text format (unformatted)
            - FASTA
            - FASTQ
      output:
        - data: Sequence alignment (nucleic acid)
        - data: Sequence alignment report
          formats:
            - SAM
            - Bowtie alignment report format