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.
© The Author(s) 2022. Published by Oxford University Press.