Mash: fast genome and metagenome distance estimation using MinHash View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-12

AUTHORS

Brian D. Ondov, Todd J. Treangen, Páll Melsted, Adam B. Mallonee, Nicholas H. Bergman, Sergey Koren, Adam M. Phillippy

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 ). More... »

PAGES

132

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13059-016-0997-x

DOI

http://dx.doi.org/10.1186/s13059-016-0997-x

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1050687712

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/27323842


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