---
ontology: EDAM (1.13)
topic:
  - Genomics
scopes:
  - name: summary
    function:
      - Genome indexing
      - Sequence alignment
    input:
      - data: Nucleic acid sequence (raw)
        format: [FASTA, FASTQ]
    output:
      - data: Sequence alignment (nucleic acid)
        format: [SAM]
  - name: bowtie-build
    function:
      - Genome indexing
    input:
      - data: Nucleic acid sequence (raw)
        format: [FASTA]
    output:
      - data: Genome index
        format:
          - ebwt
          - ebwtl
  - name: bowtie-inspect
    function:
      - Sequence retrieval
      - Metadata retrieval
      - Data index analysis
    input:
      - data: Genome index
        format: [ebtw, ebtwl]
    output:
      - data: Nucleic acid sequence (raw)
        output: [FASTA, plain text format (unformatted)]
  - name: bowtie
    function:
      - Sequence database search (by sequence using word-based methods)
      - Sequence alignment generation
    input:
      - data: Genome index
        format: [ebtw, ebtwl]
      - data: Nucleic acid sequence (raw)
        format:
          - plain text format (unformatted)
          - FASTA
          - FASTQ
    output:
      - data: Sequence alignment (nucleic acid)
        format: [SAM]
      - data: Sequence alignment report
        format:
          - plain text format (unformatted)
          - Bowtie alignment report format
