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

Katedra Algorytmiki i Oprogramowania (RAU/RAU5)

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

Wyniki badań: Wkład do czasopisma › Artykuł › recenzja

7 Cytowania z bazy Scopus

Abstrakt

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.

Język oryginału	angielski
Strony (od–do)	4423-4425
Liczba stron	3
Czasopismo	Bioinformatics
Tom	38
Numer wydania	18
Identyfikatory DOI	https://doi.org/10.1093/bioinformatics/btac528
Status publikacji	Opublikowano - 15 wrz 2022

Obszary tematyczne ASJC Scopus

Statystyka i prawdopodobieństwo
Biochemia
Biologia molekularna
Zastosowania informatyki
Teoria i matematyka obliczeń
Matematyka obliczeniowa

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10.1093/bioinformatics/btac528

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Cytowanie

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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

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JF - Bioinformatics

IS - 18

ER -

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

Abstrakt

Obszary tematyczne ASJC Scopus

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