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Translate object properties to Bowtie 2 options



S = getBowtie2Command(object) returns a character vector S, representing the Bowtie 2 option syntax that corresponds to the modified object properties. By default, the function translates only the modified properties.

getBowtie2Command 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.


S = getBowtie2Command(object,'IncludeAll',TF) specifies whether to translate all the object properties (true) or only the modified properties (false).


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Create a Bowtie2AlignOptions object.

 alignOpt = Bowtie2AlignOptions;

Modify the object properties. For example, specify to trim four residues from the 3' and 5' ends before aligning.

 alignOpt.Trim3 = 4;
 alignOpt.Trim5 = 4;

Retrieve the equivalent Bowtie 2 option syntax for the modified properties.

ans =

    '-3 4 -5 4'

Input Arguments

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Bowtie 2 options object, specified as a Bowtie2AlignOptions, Bowtie2InspectOptions, or Bowtie2BuildOptions object.

Example: alignOpt

Flag to translate all object properties, specified as true or false. If true, the function translates all the object properties. If false, the function translates only the modified properties.

Example: true

Data Types: logical

Output Arguments

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Bowtie 2 option syntax [1], returned as a character vector. The syntax is prefixed by one or two dashes.


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

Version History

Introduced in R2018a