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.
