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© Research
Publication : Bioinformatics

The K-mer File Format: a standardized and compact disk representation of sets of k-mers

Team: Bioinformatics and Biostatistics HUB
Team: Sequence Bioinformatics
Member: Yoann Dufresne
Member: Rayan Chikhi
Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Bioinformatics - 29 Jul 2022

Yoann Dufresne, Teo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, Marek Kokot, Paul Medvedev, Sebastian Deorowicz, Rayan Chikhi

Link to Pubmed [PMID] – 35904548

Link to HAL – inria-03891410

Link to DOI – 10.1093/bioinformatics/btac528

Bioinformatics, 2022, 38 (18), pp.4423-4425. ⟨10.1093/bioinformatics/btac528⟩

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: Format specification, C++/Rust API, tools: https://github.com/Kmer-File-Format/.