To build Bowtie 2 index select the Tools ‣ Align to reference ‣ Build index 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:
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.