Bowtie 2
Bowtie 2 is a popular, ultrafast, and memory-efficient tool for aligning sequencing reads to long reference sequences. Click this link to open the Bowtie 2 homepage. Bowtie 2 is embedded as an external tool into UGENE.
Open the Tools ‣ Align to reference submenu of the main menu.
Select the Align short reads item to align short reads to a DNA sequence.
Alternatively, select the Build index item to build an index for a DNA sequence, which can be used to optimize the alignment of the short reads to the sequence.