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

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

doi:10.1093/bioinformatics/btac528

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

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

Department of Algorithmics and Software (RAU/RAU5)

Université Paris Cité
Irisa - Umr
Heinrich Heine University Düsseldorf
Pennsylvania State University

Research output: Contribution to journal › Article › peer-review

7 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	4423-4425
Number of pages	3
Journal	Bioinformatics
Volume	38
Issue number	18
DOIs	https://doi.org/10.1093/bioinformatics/btac528
Publication status	Published - 15 Sept 2022

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btac528

Cite this

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abstract = "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{\texttimes} compared to other formats, and bringing interoperability across tools.",

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AU - Dufresne, Yoann

AU - Lemane, Teo

AU - Marijon, Pierre

AU - Peterlongo, Pierre

AU - Rahman, Amatur

AU - Kokot, Marek

AU - Medvedev, Paul

AU - Deorowicz, Sebastian

AU - Chikhi, Rayan

PY - 2022/9/15

Y1 - 2022/9/15

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/85136559310

U2 - 10.1093/bioinformatics/btac528

DO - 10.1093/bioinformatics/btac528

M3 - Article

AN - SCOPUS:85136559310

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SP - 4423

EP - 4425

JO - Bioinformatics

JF - Bioinformatics

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ER -

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

Abstract

ASJC Scopus subject areas

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