Building Index for Bowtie

To build a Bowtie 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 Map short reads method parameter to Bowtie.

The dialog looks as follows:

The following parameters are required:

• 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. This parameter is required.