Mash
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  • Supporting Data
  • Tutorials
  • Sketches
  • Distance Estimation
Mash
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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
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© Copyright 2015, Brian Ondov, Todd Treangen, Adam Phillippy Revision c081d852.

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