To build BWA-MEM index select the Tools ‣ NGS data analysis ‣ Build index for reads mapping item in the main menu. The Build Index dialog will appears. Set the Map short reads method parameter to BWA-MEM.

The dialog looks as follows:

     <img src="/wiki/download/attachments/65930886/BWA-MEM.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 — file to save index to. This parameter is required.

Index algorithm (-a) — Algorithm for constructing BWA index. Available options are:

It implements three different algorithms

The value "autodetect" by default means that the index (one of three) is chosen automatically depending on the length of the sequence.