YAHA is a flexible, sensitive and accurate hash-based DNA aligner for relatively long queries that operates in three distinct modes. It can output all the alignments found for each query, only the set of alignments that optimally cover each query, or add alignments that are similar to those that optimally cover the query.
Ira Hall Lab at University of Virginia
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Bioinformatics. 2012 Oct 1;28(19):2417-24. Epub 2012 Jul 24.
YAHA: fast and flexible long-read alignment with optimal breakpoint detection.
Faust GG1, Hall IM.