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

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/.

Domaines

Bio-informatique [q-bio.QM]

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btac528.pdf (450.93 Ko)

Origine	Publication financée par une institution
Licence	Paternité

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https://inria.hal.science/hal-03885245

Soumis le : vendredi 9 décembre 2022-11:04:08

Dernière modification le : jeudi 7 novembre 2024-13:44:03

Archivage à long terme le : vendredi 10 mars 2023-18:35:53

Dates et versions

hal-03885245 , version 1 (09-12-2022)

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Paternité

Identifiants

HAL Id : hal-03885245 , version 1
DOI : 10.1093/bioinformatics/btac528
PUBMED : 35904548
PUBMEDCENTRAL : PMC9477520

Citer

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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