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');