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Mash Screen: high-throughput sequence containment estimation for genome discovery

Year: 2019
Type: article
Abstract: The MinHash algorithm has proven effective for rapidly estimating the resemblance of two genomes or metagenomes. However, this method cannot reliably estimate the containment of a genome within a metagenome. Here, we describe an online algorithm capable of measuring the containment of genomes and proteomes within either assembled or unassembled sequencing read sets. We describe several use cases, including contamination screening and retrospective analysis of metagenomes for novel genome discovery. Using this tool, we provide containment estimates for every NCBI RefSeq genome within every SRA metagenome and demonstrate the identification of a novel polyomavirus species from a public metagenome.
DOI: 10.1186/s13059-019-1841-x
Authors: Brian D Ondov, Gabriel J Starrett, Anna Sappington, Aleksandra Kostic, Sergey Koren, Christopher B Buck, Adam M Phillippy
Institutions: National Human Genome Research Institute, University of Maryland, College Park, National Institutes of Health, National Cancer Institute, Massachusetts Institute of Technology, Princeton University
Language: English
Open Access status: gold
Estimated APC paid: $3,490
OpenAlex ID: W2987650093
FWCI: 12.24
Cites: 40
Cited by: 323
Related to: 10