The K-mer File Format: a standardized and compact disk representation of sets of k-mers.
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- Record sourced from PubMed, PMID 35904548.
- Also identified by DOI 10.1093/bioinformatics/btac528 and PMC identifier 9477520.
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Abstract
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. Format specification, C++/Rust API, tools: https://github.com/Kmer-File-Format/. Supplementary data are available at Bioinformatics online.
Medical subject headings
- Software
- Algorithms