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 ‣ DNA assembly submenu of the main menu.
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Select the Align short reads item to align short reads to a DNA sequence or Build index item to build an index for a DNA sequence which can be used to optimize aligning short reads to the sequence.