Fast genome and metagenome distance estimation using MinHash

Publications

Mash: fast genome and metagenome distance estimation using MinHash. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Genome Biol. 2016 Jun 20;17(1):132. doi: 10.1186/s13059-016-0997-x.

Mash Screen: high-throughput sequence containment estimation for genome discovery. Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, Phillippy AM. Genome Biol. 2019 Nov 5;20(1):232. doi: 10.1186/s13059-019-1841-x.

• Supporting Data

Downloads

• Linux/OSX binaries and source
• RefSeq sketch database

Documentation

• Tutorials
  • Simple distance estimation
  • Saving time by sketching first
  • Pairwise comparisons with compound sketch files
  • Querying read sets against an existing RefSeq sketch
  • Screening a read set for containment of RefSeq genomes
• Sketches
  • Reduced representations with MinHash tables
  • Strand and alphabet
  • Sketching read sets
  • Working with sketch files
• Distance Estimation
  • MinHash Jaccard estimation
  • Mash distance formulation
  • Assessing significance with p-values