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.

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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.