Building Index for Bowtie 2

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

The dialog looks as follows:

The following parameters are available:

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

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