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To build Bowtie 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.

The dialog looks as follows:

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     <img src="/wiki/download/attachments/4227711/Building Index for Bowtie.png"/>
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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.

Colorspace (–color) — the input is read in colorspace, colors are encoded as characters A/C/G/T (A=blue, C=green, G=orange, T=red).