wfmash: a pangenome-scale aligner

wfmash is an aligner for pangenomes based on sparse homology mapping and wavefront inception.

wfmash uses a variant of  MashMap to find large-scale sequence homologies. It then obtains base-level alignments using WFA, via the wflign hierarchical wavefront alignment algorithm.

wfmash is designed to make whole genome alignment easy. On a modest compute node, whole genome alignments of gigabase-scale genomes should take minutes to hours, depending on sequence divergence. It can handle high sequence divergence, with average nucleotide identity between input sequences as low as 70%.

wfmash is the key algorithm in pggb (the PanGenome Graph Builder), where it is applied to make an all-to-all alignment of input genomes that defines the base structure of the pangenome graph. It can scale to support the all-to-all alignment of hundreds of human genomes.