MashMap implements a fast and approximate algorithm for computing local
alignment boundaries between long DNA sequences. It can be useful for mapping
genome assembly or long reads (PacBio/ONT) to reference genome(s). Given a
minimum alignment length and an identity threshold for the desired local
alignments, Mashmap computes alignment boundaries and identity estimates using
k-mers. It does not compute the alignments explicitly, but rather estimates an
unbiased k-mer based Jaccard similarity using a combination of minmers (a novel
winnowing scheme) and MinHash. This is then converted to an estimate of sequence
identity using the Mash distance. An appropriate k-mer sampling rate is
automatically determined using the given minimum local alignment length and
identity thresholds.