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Bowtie is a popular short read aligner. Click this link to open Bowtie homepage. Bowtie is embedded as an external tool into UGENE.

Open Tools ‣ DNA Assembly submenu of the main menu.

Select the Align short reads item to align short reads to a DNA sequence using Bowtie. Or select the Build index item to build an index for a DNA sequence which can be used to optimize aligning of the short reads to the sequence.

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