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Create Bowtie 2 index files from reference sequences



bowtie2build(referenceFileNames,indexBaseName) builds Bowtie2 index files from the reference sequence information saved in the FASTA files specified by referenceFileNames.

bowtie2build requires the Bowtie 2 Support Package for Bioinformatics Toolbox™. If this support package is not installed, then the function provides a download link. For details, see Bioinformatics Toolbox Software Support Packages.


bowtie2build(___,buildOptions) uses the additional options specified by buildOptions. Specify these options after all other input arguments.


flag = bowtie2build(___) returns an exit flag of the function using any of the input arguments in the previous syntaxes.


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Build a set of index files for the Drosophila genome. An error message appears if you do not have the Bioinformatics Toolbox Interface for Bowtie Aligner support package installed when you run the function. Click the provided link to download the package from the Add-on menu.

For this example, the reference sequence Dmel_chr4.fa is already provided with the toolbox.

status = bowtie2build('Dmel_chr4.fa', 'Dmel_chr4_index');

If the index build is successful, the function returns 0 and creates the index files (*.bt2) in the current folder. The files have the prefix 'Dmel_chr4_index'.

You can specify different options by using a Bowtie2BuildOptions object or by passing in a Bowtie 2 syntax string. For instance, you can specify whether to force the creation of a large index even if the reference is less than four billion nucleotides long as follows.

buildOpt = Bowtie2BuildOptions;

Set the ForceLargeIndex option to true.

buildOpt.ForceLargeIndex = true;

Build the index files using the specified option.

bowtie2build('Dmel_chr4.fa', 'Dmel_chr4_index_large',buildOpt);

Alternatively, you can pass in a Bowtie 2 syntax string.

flag = bowtie2build('Dmel_chr4.fa', 'Dmel_chr4_index_large2','--large-index');

Input Arguments

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Names of files with reference sequence information, specified as a string, character vector, string array, or cell array of character vectors.

Example: 'Dmel_chr4.fa'

Data Types: char | string | cell

Base name (prefix) of the reference index files, specified as a character vector or string. The index files are in the BT2 or BT21 format.

Example: 'Dmel_chr4'

Data Types: char | string

Options to build index files, specified as a character vector, string, or Bowtie2BuildOptions object. The character vector or string must be in the Bowtie 2 option syntax (prefixed by one or two dashes) [1].

For a Bowtie2BuildOptions object, only the modified properties are used to run the function.

Example: '--trim5 10 -s 5'

Output Arguments

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Exit status of the function, returned as an integer. flag is 0 if the function runs without errors or warning. Otherwise, it is nonzero.


[1] Langmead, B., and S. Salzberg. "Fast gapped-read alignment with Bowtie 2." Nature Methods. 9, 2012, 357–359.

Version History

Introduced in R2018a