Mash: fast genome and metagenome distance estimation using MinHash

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 whic...

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Bibliographic Details
Published in:Genome Biology Vol. 17; no. 1; p. 132
Main Authors: Ondov, Brian D., Treangen, Todd J., Melsted, Páll, Mallonee, Adam B., Bergman, Nicholas H., Koren, Sergey, Phillippy, Adam M.
Format: Journal Article
Language:English
Published: London BioMed Central 20.06.2016
Springer Nature B.V
Subjects:
Animal Genetics and Genomics
Automation
Bioinformatics
Biomedical and Life Sciences
Cluster Analysis
Data collection
Databases, Nucleic Acid
Estimates
Evolution, Molecular
Evolutionary Biology
Genome
Genomes
Genomics
Genomics - methods
Human Genetics
Library collections
Life Sciences
mash
Metagenome
metagenomics
Metagenomics - methods
Microbial Genetics and Genomics
Mutation
nanopores
Phylogeny
Plant Genetics and Genomics
Privacy
Software
Comparative genomics
Metagenomics
Alignment
Nanopore
Genomic distance
Sequencing
ISSN:1474-760X, 1474-7596, 1474-760X
Online Access:Get full text
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Description
Summary: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 ).
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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-016-0997-x