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bowtiebuild

(To be removed) Generate index using Burrows-Wheeler transform

bowtiebuild will be removed in a future release. Use bowtie2 and bowtie2build instead.

Description

example

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.

example

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

Examples

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Download the E. coli genome from NCBI.

getgenbank('NC_008253','tofile','NC_008253.fna','SequenceOnly',true)

Built a Bowtie index with the base name ECOLI.

bowtiebuild('NC_008253.fna','ECOLI')

Input Arguments

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

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

Additional bowtiebuild options, specified as a character vector or string for any valid bowtiebuild options. Type bowtiebuild('--help') for available options.

Example: '-t 5 -C'

Tips

Version History

Introduced in R2012b

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Not recommended starting in R2022a