yaha

find split-read mappings on single-end queries

yaha is an open source, flexible, sensitive and accurate DNA aligner designed for single-end reads. It supports three major modes of operation: * The default “Optimal Query Coverage” (-OQC) mode reports the best set of alignments that cover the length of each query. * Using “Filter By Similarity” (-FBS), along with the best set of alignments, yaha will also output alignments that are highly similar to an alignment in the best set. * Finally, yaha can output all the alignments found for each query. The -OQC and -FBS modes are specifically tuned to form split read mappings that can be used to accurately identify structural variation events (deletions, duplications, insertions or inversions) between the subject query and the reference genome.