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 ‣ NGS data analysis submenu of the main menu.
Select the Map reads to reference item to align short reads to a DNA sequence using Bowtie 2.
Alternatively, select the Build index to reads mapping option for a DNA sequence, which can be used to optimize the alignment of the short reads to the sequence.