A flexible, sensitive and accurate hash-based DNA aligner for relatively long queries that operates in three distinct modes. YAHA uses a directed acyclic graph to find the optimal set of alignments that cover a query using a biologically relevant breakpoint penalty. It can also report multiple mappings per defined segment of the query. YAHA detects more breakpoints in less time than BWA-SW across all SV classes, and especially excels at complex SVs comprising multiple breakpoints.
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.