Mash: fast genome and metagenome distance estimation using MinHash

By Brian D. Ondov, Todd J. Treangen, Páll Melsted, Adam B. Mallonee, Nicholas H. Bergman, Sergey Koren, Adam M. Phillippy. Genome Biology, 2015

2,878 citations recorded by the source corpus.

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).

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1582cda4b0d8b962f6920c24a476650032ea9875

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Citations in the corpus

A review of methods and databases for metagenomic classification and assembly (2019, methodology): “An alternative approach for metagenomics profiling is using the overlap of MinHash signatures [89] as implemented in Mash [83] and sourmash [84].”
dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication (2017, methodology): “, 2015), Mash (Ondov et al., 2016) for fast grouping of similar genomes, gANI (Varghese et al.”
Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI (2018, positive): “First, incoming genomes are compared to the existing type assemblies using a fast MinHash-based k-mer comparison [15, 16].”
IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets (2017, positive): “Therefore, to ensure our ability to handle the anticipated larger number of predictions needed thanks to the new batch submission system, IslandViewer 4 now integrates MASH (32) – a recently published tool for efficient measure of genome similarity – as a replacement of CVTree (31).”
MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies (2018, positive): “MOB-cluster uses mash dist [22] with default parameters to calculate all pairwise genomic distances for each plasmid contained in the closed plasmid reference database.”
Producing polished prokaryotic pangenomes with the Panaroo pipeline (2020, methodology): “We have included a wrapper for the popular Mash and Mash screen algorithms which generates diagnostic plots for quality control prior to running the Panaroo pipeline (46, 47).”
Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease (2019, positive): “The sketch file was then compared to all the initial phage genome sequences to generate the ANI matrix using the mash distance command using default settings.”
Clustering huge protein sequence sets in linear time (2017, background): “At 50% identity, Linclust clusters the 123 million sequences 10 times faster than Linclust/MMseqs2 and, by extrapolation, 2300 times faster than UCLUST, 720 times faster than MMseqs, 4600 times faster than CD-HIT, 1600 times faster than DIAMOND [12], 69 000 times faster than MASH [13], and 26 000 ti”
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2020, methodology): “For species having more than 200 reference genomes available, the pangenome is made using a representative subset of 200 genomes maximizing the Mash distances between them (Ondov et al., 2016) .”
Disease-induced assemblage of a plant-beneficial bacterial consortium (2018, positive): “gov/ refseq/) were estimated using MASH [37].”
Fast and flexible bacterial genomic epidemiology with PopPUNK (2018, methodology): “We use Mash (Ondov et al. 2016) with a default sketch size of 10 4 to efficiently calculate p match for every second k -mer size from k = k min to k = k max (29, by default).”
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities (2019, methodology): “PATRIC provides a service called the Similar Genome Finder to allow researchers to rapidly identify similar genome sequences us-ing Mash (45).”