Maligner

Maligner is a software tool for aligning optical mapping datasets that discovers structural variants and potentiates sequence assembly of genomes. It aligns both single molecule restriction maps (Rmaps) and in silico restriction maps of sequence contigs to a reference. Maligner provides two modes of alignment: an efficient, sensitive dynamic programming implementation that scales to large eukaryotic genomes, and a faster indexed based implementation for finding alignments with unmatched sites in the reference but not the query.