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 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 ).
National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA.
Brian D
BD
Ondov
National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA.
Todd J
TJ
Treangen
Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavik, Iceland.
Páll
P
Melsted
National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA.
Adam B
AB
Mallonee
National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA.
Nicholas H
NH
Bergman
Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Sergey
S
Koren
Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA. adam.phillippy@nih.gov.
Adam M
AM
Phillippy
D016000:Cluster Analysis; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D016678:Genome; D023281:Genomics / Q000379:methods*; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D010802:Phylogeny; D012984:Software
Alignment; Comparative genomics; Genomic distance; Metagenomics; Nanopore; Sequencing