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MasHmap

Description

mashmap website

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 a k-mer based Jaccard similarity using a combination of Minimizers and MinHash.

Environment Modules

Run module spider mashmap to find out what environment modules are available for this application.

Environment Variables

  • HPC_MASHMAP_DIR - installation directory
  • HPC_MASHMAP_BIN - executable directory

Categories

phylogenetics