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Generate index using Burrows-Wheeler transform


  • bowtiebuild(input,indexBaseName)
  • bowtiebuild(input,indexBaseName,'BowtieBuildOptions',options)



bowtiebuild(input,indexBaseName) builds an index using the reference sequence(s) in input, and saves it to the index file indexBaseName.

    Note:   bowtiebuild runs on Mac and UNIX® platforms only.

bowtiebuild(input,indexBaseName,'BowtieBuildOptions',options) specifies additional options.


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Download the E. coli genome from NCBI.


Built a Bowtie index with the base name ECOLI.


Input Arguments

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FASTA-formatted files with the reference sequences to be indexed, specified as a character vector or cell array of character vectors. Use a cell array of character vectors to specify multiple files.

Name for indexed reference file, specified as a character vector containing the path and base name for the resulting Bowtie index file.

Additional bowtiebuild options, specified as any valid bowtiebuild option. Type bowtiebuild('--help') for available options.

More About

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Introduced in R2012b

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