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Bowtie2BuildOptions

Contain options to create Bowtie 2 index files from reference sequences

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Description

A Bowtie2BuildOptions object contains options to run the bowtie2build function that builds Bowtie 2 index files from reference sequences.

Creation

Syntax

buildOptions = Bowtie2BuildOptions
buildOptions = Bowtie2BuildOptions(Name,Value)
buildOptions = Bowtie2BuildOptions(S)

Description

buildOptions = Bowtie2BuildOptions creates a Bowtie2BuildOptions object with default property values.

Bowtie2BuildOptions 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.

example

buildOptions = Bowtie2BuildOptions(Name,Value) sets properties using one or more name-value pairs. Enclose each property name in quotes. For example, buildOptions = Bowtie2BuildOptions('ForceLargeIndex',true) specifies to force the creation of a large index even if the reference is less than 4 billion nucleotides long.

example

buildOptions = Bowtie2BuildOptions(S) specifies optional parameters in a character vector or string S.

example

Input Arguments

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

Data Types: char | string

Properties

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Boolean indicator to build only the 3.bt2 and 4.bt2 files that correspond to the bitpacked version of reference sequences, specified as true or false.

Example: 'BuildOnlyReference',true

Data Types: logical

Boolean indicator to omit building the 3.bt2 and 4.bt2 files that correspond to the bitpacked version of reference sequences, specified as true or false.

Example: 'BuildNoReference',true

Data Types: logical

Additional options not included in the object properties, specified as a character vector. The character vector must be in the Bowtie 2 option syntax (prefixed by one or two dashes). The default value is an empty character vector ''.

Example: 'ExtraBowtie2Command','--version'

Data Types: char | string

Boolean indicator to force building a large index even if the reference is less than four billion nucleotides long, specified as true or false.

Example: 'ForceLargeIndex',true

Data Types: logical

Number of parallel threads to build the index files, specified as a positive integer. Threads are run on separate processors or cores. Increasing the number of threads provides significant speed-up (close to linear) but also increases the memory footprint.

Example: 'NumThreads',4

Data Types: double

Number of Burrows-Wheeler rows to mark when building the index files, specified as a positive integer. To map the alignment back to positions on the reference sequences, the function uses this number to mark some of the rows in the Burrows-Wheeler algorithm with their corresponding location on the genome. The function marks every 2n, where n is the offrate.

Increasing the number of marked rows makes the reference position lookups faster, but requires more memory.

Example: 'Offrate',6

Data Types: double

Number to set the seed in the pseudo-random number generator, specified as a nonnegative integer.

Example: 'Seed',3

Data Types: double

Object Functions

getBowtie2CommandTranslate object properties to Bowtie 2 options
getBowtie2TableRetrieve table with object properties and equivalent Bowtie 2 options
runBuild Bowtie 2 index files

Examples

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Build a set of index files for the Drosophila genome. An error message appears if you do not have the Bowtie 2 Support Package for Bioinformatics Toolbox 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');

References

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

Version History

Introduced in R2018a

See Also

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