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bowtiebuild

Generate index using Burrows-Wheeler transform

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

Introduced in R2012b