topic: topic_0622 Genomics
scope: summary
 function: operation_3212 Genome indexing (Burrows-Wheeler)
 function: operation_0292 Sequence alignment generation
 input: data_2975 Nucleic acid sequence (raw)
 input: format_1929 FASTA
 input: format_1930 FASTQ
 output: data_1383 Sequence alignment (nucleic acid)
 output: format_2573 SAM
scope: bowtie-build
 function: operation_3212 Genome indexing (Burrows-Wheeler)
 input: data_2975 Nucleic acid sequence (raw)
 input: format_1929 FASTA
 output: data_3210 Genome index
 output: ??? Bowtie index format EBWT
 output: ??? Bowtie long index format EBTWL
scope: bowtie-inspect
 function: operation_1813 Sequence retrieval
 function: operation_0304 Metadata retrieval
 function: operation_0228 Data index analysis
 input: data_3210 Genome index
 input: ??? Bowtie index format EBWT
 input: ??? Bowtie long index format EBTWL
 output: data_2975 Nucleic acid sequence (raw)
 output: format_1929 FASTA
 output: format_1964 plain text format (unformatted)
scope: bowtie
 function: operation_0350 Sequence database search (by sequence using word-based methods)
 function: operation_0292 Sequence alignment generation
 input: data_3210 Genome index
 input: data_2975 Nucleic acid sequence (raw)
 input: format_1964 plain text format (unformatted)
 input: format_1929 FASTA
 input: format_1930 FASTQ
 output: data_1383 Sequence alignment (nucleic acid)
 output: data_0867 Sequence alignment report
 output: format_2573 SAM
 output: ??? Bowtie alignment report format

topic: topic_0622 Genomics
function: operation_3212 Genome indexing (Burrows-Wheeler)
function: operation_0292 Sequence alignment generation
input: data_2975 Nucleic acid sequence (raw)
input: format_1929 FASTA
input: format_1930 FASTQ
output: data_1383 Sequence alignment (nucleic acid)
output: format_2573 SAM
