STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions
Kenneth Katz, Oleg Shutov, Richard T. Lapoint, Michael Kimelman, J. Rodney Brister, Christopher D. O’Sullivan
Abstract
Sequence Read Archive submissions to the National Center for Biotechnology Information often lack useful metadata, which limits the utility of these submissions. We describe the Sequence Taxonomic Analysis Tool (STAT), a scalable k-mer-based tool for fast assessment of taxonomic diversity intrinsic to submissions, independent of metadata. We show that our MinHash-based k-mer tool is accurate and scalable, offering reliable criteria for efficient selection of data for further analysis by the scientific community, at once validating submissions while also augmenting sample metadata with reliable, searchable, taxonomic terms.
Topics & Concepts
MetadataScalabilityk-merBiologyComputer scienceComputational biologySequence (biology)Information retrievalData scienceBioinformaticsLibrary scienceWorld Wide WebDNA sequencingDatabaseGeneticsDNAGenomics and Phylogenetic StudiesSpecies Distribution and Climate ChangeGenetic diversity and population structure