wfmash

wfmash uses a modified version of mashmap to obtain approximate mappings, and then applies a wavefront-guided global alignment algorithm for long sequences to derive an alignment for each mapping. wfmash uses the wavefront alignment algorithm for base-level alignment. This mapper is used to scaffold the pangenome, using genome segments of a given length with a specified maximum level of sequence divergence. All segments in the input are mapped to all others. This step yields alignments represented in the PAF output format, with cigars describing their base-exact alignment.