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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




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Publication for YAHA

YAHA citations


Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

BMC Genomics
PMCID: 5937819
PMID: 29690866
DOI: 10.1186/s12864-018-4683-0

[…] contigs was performed using the overlap-based (olc) assembler fermi-lite [], considering the number of reads in a 2 kbp window can be relatively small. contigs were aligned to the reference using yaha v0.1.83 [], which is optimized for finding spilt-alignments. split-alignments were allowed 75% of overlap in the contig. sv validity was then inferred from the alignment results. a deletion […]


Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

Nat Commun
PMCID: 5286201
PMID: 28117401
DOI: 10.1038/ncomms14061

[…] (version asm294v2.22). reads with 20 base pairs or more clipped were extracted using the script split_unmapped_to_fasta.pl included in the lumpy package (version 0.2.9) and were then mapped using yaha (version 0.1.83) to generate split-read alignments. the two mapped files were merged using picard-tools (version 1.105) (http://broadinstitute.github.io/picard), and all strains […]


Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

PMCID: 5167521
PMID: 27911260
DOI: 10.7554/eLife.20777.056

[…] calls bowtie2 () with the following options: ‘–local’, ‘–dovetail’, ‘–fr’, ‘-r5’, ‘-n1’. soft-clipped and unmapped reads are extracted using samblaster (), and remapped using the split read mapper yaha (), with the following options: ‘-l 11’, ‘-h 2000’, ‘-m 15’, ‘-osh’. split reads are extracted from the yaha alignment using samblaster (). alignments are then converted to bam format, sorted, […]


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

PMCID: 4592165
PMID: 26308889
DOI: 10.1038/nature14970

[…] 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 […]


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

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

[…] 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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