BWA
BWA is a fast, lightweight tool that aligns relatively short reads to a reference sequence. Click this link to open the BWA homepage. BWA is embedded as an external tool into UGENE.
Open the _Tools ‣ NGS data analysis submenu of the main menu.
Select the Map read to reference item to align short reads to a DNA sequence using BWA, or select the Build index for reads mapping item to build an index for a DNA sequence, which can be used to optimize the alignment of short reads.