---
ontology: EDAM (1.13)
topic:
 - Genomics
scopes:
 - name: summary
   function:
    - operation_3211 Genome indexing
    - operation_0292 Sequence alignment generation
   inputs:
    - data_2975 Nucleic acid sequence (raw)
    - format_1929 FASTA
    - format_1930 FASTQ
   outputs:
    - data_1383 Sequence alignment (nucleic acid)
    - format_2573 SAM
 - name: bowtie-build
   function: operation_3212 Genome indexing (Burrows-Wheeler)
   inputs:
    - data_2975 Nucleic acid sequence (raw)
    - format_1929 FASTA
   outputs:
    - data_3210 Genome index
    - ??? Bowtie index format EBWT
    - ??? Bowtie long index format EBTWL
 - name: bowtie-inspect
   function:
    - operation_1813 Sequence retrieval
    - operation_0304 Metadata retrieval
    - operation_0228 Data index analysis
   inputs:
    - data_3210 Genome index
    - ??? Bowtie index format EBWT
    - ??? Bowtie long index format EBTWL
   outputs:
    - data_2975 Nucleic acid sequence (raw)
    - format_1929 FASTA
    - format_1964 plain text format (unformatted)
 - name: bowtie
   function:
    - operation_0350 Sequence database search (by sequence using word-based methods)
    - operation_0292 Sequence alignment generation
   inputs:
    - data_3210 Genome index
    - data_2975 Nucleic acid sequence (raw)
    - format_1964 plain text format (unformatted)
    - format_1929 FASTA
    - format_1930 FASTQ
   outputs:
    - data_1383 Sequence alignment (nucleic acid)
    - data_0867 Sequence alignment report
    - format_2573 SAM
    - ??? Bowtie alignment report format
 - name: FIXME remainings of blody syntax errors
   function:
    - operation_3212 Genome indexing (Burrows-Wheeler)
    - operation_0292 Sequence alignment generation
   inputs:
    - data_2975 Nucleic acid sequence (raw)
    - format_1929 FASTA
    - format_1930 FASTQ
   outputs:
    - data_1383 Sequence alignment (nucleic acid)
    - format_2573 SAM
