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Journal Articles Bioinformatics Year : 2022

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

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. Availability: Format specification, C++/Rust API, tools: https://github.com/Kmer-File-Format/.
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hal-03885245 , version 1 (09-12-2022)

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Yoann Dufresne, Teo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, et al.. The K-mer File Format: a standardized and compact disk representation of sets of k-mers. Bioinformatics, 2022, 38 (18), pp.4423-4425. ⟨10.1093/bioinformatics/btac528⟩. ⟨hal-03885245⟩
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