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Genome Biol. 2016 Jun 20;17(1):132. doi: 10.1186/s13059-016-0997-x.

Mash: fast genome and metagenome distance estimation using MinHash.

Author information

1
National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA.
2
Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavik, Iceland.
3
Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
4
Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA. adam.phillippy@nih.gov.

Abstract

Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P value significance test, enabling the efficient clustering and search of massive sequence collections. Mash reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated. We demonstrate several use cases, including the clustering of all 54,118 NCBI RefSeq genomes in 33 CPU h; real-time database search using assembled or unassembled Illumina, Pacific Biosciences, and Oxford Nanopore data; and the scalable clustering of hundreds of metagenomic samples by composition. Mash is freely released under a BSD license ( https://github.com/marbl/mash ).

KEYWORDS:

Alignment; Comparative genomics; Genomic distance; Metagenomics; Nanopore; Sequencing

PMID:
27323842
PMCID:
PMC4915045
DOI:
10.1186/s13059-016-0997-x
[Indexed for MEDLINE]
Free PMC Article

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