The K-mer File Format: a standardized and compact disk representation of sets of <i>k</i>-mers-Reference-Cited by-同舟云学术

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

Published:2022-07-29 Issue:18 Volume:38 Page:4423-4425
ISSN:1367-4803
Container-title:Bioinformatics
language:en
Short-container-title:

Author:

Dufresne Yoann¹^ORCID,Lemane Teo²^ORCID,Marijon Pierre³,Peterlongo Pierre²^ORCID,Rahman Amatur⁴,Kokot Marek⁵,Medvedev Paul⁴⁶⁷^ORCID,Deorowicz Sebastian⁵,Chikhi Rayan¹

Affiliation:

1. Computational Biology Department, Institut Pasteur, Université Paris Cité , F-75015 Paris, France

2. Univ Rennes, Inria, CNRS, IRISA—UMR , 6074 Rennes, France

3. Heinrich Heine University Düsseldorf Medical Faculty Institute for Medical Biometry and Bioinformatic , Düsseldorf 40225, Germany

4. Department of Computer Science and Engineering, The Pennsylvania State University , State College 16802, USA

5. Department of Algorithmics and Software, Silesian University of Technology, Gliwice , PL-44-100 Akademicka 16, Poland

6. Department of Biochemistry and Molecular Biology, The Pennsylvania State University , State College 16801, USA

7. Huck Institutes of the Life Sciences, The Pennsylvania State University , State College 16802, USA

Abstract

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. Availability and implementation Format specification, C++/Rust API, tools: https://github.com/Kmer-File-Format/. Supplementary information Supplementary data are available at Bioinformatics online.

Funder

ANR Inception

PRAIRIE

National Science Centre

National Science Foundation

European Union’s Horizon 2020 Research and Innovation Programme

Marie Skłodowska-Curie

Publisher

Oxford University Press (OUP)

Subject

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

Link

https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btac528/45290957/btac528.pdf

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