The K-mer File Format: a standardized and compact disk representation of sets of<i>k</i>-mers
Yoann Dufresne, Téo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, Marek Kokot, Paul Medvedev, Sebastian Deorowicz, Rayan Chikhi
Abstract
SUMMARY: Bioinformatics applications increasingly rely on ad hoc disk storage of k-mer sets, e.g. for de Bruijn graphs or alignment indexes. Here, we introduce the K-mer File Format as a general lossless framework for storing and manipulating k-mer sets, realizing space savings of 3-5× compared to other formats, and bringing interoperability across tools. AVAILABILITY AND IMPLEMENTATION: Format specification, C++/Rust API, tools: https://github.com/Kmer-File-Format/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Topics & Concepts
k-merComputer scienceRepresentation (politics)BiologyDNAGeneticsDNA sequencingLawPoliticsPolitical scienceAdvanced Data Storage TechnologiesAlgorithms and Data CompressionAdvanced Database Systems and Queries