Difference between revisions of "YAHA"

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* Validated 4/5/2018

Revision as of 18:50, 5 April 2018


yaha website  

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.

Required Modules

System Variables

  • HPC_{{#uppercase:yaha}}_DIR


If you publish research that uses yaha you have to cite it as follows:

Citation: Faust GG and Hall IM. YAHA: fast and flexible long-read alignment with optimal breakpoint detection. Bioinformatics (2012) 28(19): 2417-2424. Epub 2012 Jul 24. doi:10.1093/bioinformatics.


  • Validated 4/5/2018