Unipro UGENE User Manual
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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 the Map short reads method parameter to Bowtie.

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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).