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YAHA specifications


Unique identifier OMICS_04675
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes




No version available

Publication for YAHA

YAHA citations


Orientation Specific Joining of AID initiated DNA Breaks Promotes Antibody Class Switching

PMCID: 4592165
PMID: 26308889
DOI: 10.1038/nature14970

[…] pipeline on libraries made with CH12F3 cells. To reflect additional genome modifications (e.g. Sμ(INV) shown in ), mm9 genome sequence was modified accordingly.Best-path searching algorithm (based on YAHA read aligner and breakpoint detector, Faust et al., 2012) was used to select optimal sequence alignments from Bowtie2 reported top alignments with an alignment score above 50, which represents a […]


Local sequence assembly reveals a high resolution profile of somatic structural variations in 97 cancer genomes

Nucleic Acids Res
PMCID: 4787836
PMID: 26283183
DOI: 10.1093/nar/gkv831

[…] mplications for the development of cancer type-specific treatments.At present laSV employs BWA to align assembled contigs to the reference and predict SV breakpoints. There are other methods, such as YAHA () and AGE (), that specialize in aligning long sequences and detecting potential breakpoints. In the future it would be interesting to explore how laSV performs using these software for contigs […]


Genome wide detection of DNA double stranded breaks induced by engineered nucleases

Nat Biotechnol
PMCID: 4320661
PMID: 25503383
DOI: 10.1038/nbt.3101

[…] ed a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition, typically finding the bait and prey alignments. This approach was inspired by the YAHA read aligner and breakpoint detector. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot […]


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YAHA institution(s)
Department of Computer Science, Genomics, University of Virginia, Charlottesville, VA, USA; Department of Biochemistry and Molecular Genetics Genomics, University of Virginia, Charlottesville, VA, USA; Center for Public Health, Genomics, University of Virginia, Charlottesville, VA, USA
YAHA funding source(s)
This research was supported by an National Institute of Health (NIH) New Innovator Award DP2OD006493-01, a Burroughs Wellcome Fund Career Award and an NIH Biotechnology Training Grant T32 GM08715.

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