To build Bowtie 2 index select the Tools ‣ NGS data analysis ‣ Build index for reads mapping item in the main menu. The Build Index dialog appears. Set the Align short reads method parameter to Bowtie 2.

The dialog looks as follows:

     <img src="/wiki/download/attachments/6062137/Building Index for Bowtie 2.png"/>

There are the following parameters:

Reference sequence — DNA sequence to which short reads would be aligned to. This parameter is required.

Index file name — a file to save the created index to. This parameter is required.