The UGENE Genome Aligner is a fast short read aligner. It aligns DNA sequences of various lengths to the reference genome with configurable mismatch rate.
It is available from 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 or Build index for reads mapping item to build an index for a DNA sequence which can be used to optimize aligning short reads to the sequence.