YAHA

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. These latter two modes are especially useful for finding split-read mappings used to accurately identify structural variation events.

For questions, suggestions or bug reports concerning YAHA, contact Greg Faust (gf4ea@virginia.edu).

Downloads: (right-click and select “Save Link As…”)

YAHA72: Latest Release Feb 14, 2013 (multi-thread support added):
YAHA_User_Guide.0.1.72.pdf
YAHA.0.1.72.tar.gz

YAHA64: Released Dec 6, 2012:
YAHA_User_Guide.0.1.64.pdf
YAHA.0.1.64.tar.gz

YAHA38: Initial release including data files used in Bioinformatics publication, May 6, 2012:
YAHA.0.1.38.tar.gz