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

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 o...

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Autores principales: Dufresne, Yoann, Lemane, Teo, Marijon, Pierre, Peterlongo, Pierre, Rahman, Amatur, Kokot, Marek, Medvedev, Paul, Deorowicz, Sebastian, Chikhi, Rayan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9477520/
https://www.ncbi.nlm.nih.gov/pubmed/35904548
http://dx.doi.org/10.1093/bioinformatics/btac528
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author Dufresne, Yoann
Lemane, Teo
Marijon, Pierre
Peterlongo, Pierre
Rahman, Amatur
Kokot, Marek
Medvedev, Paul
Deorowicz, Sebastian
Chikhi, Rayan
author_facet Dufresne, Yoann
Lemane, Teo
Marijon, Pierre
Peterlongo, Pierre
Rahman, Amatur
Kokot, Marek
Medvedev, Paul
Deorowicz, Sebastian
Chikhi, Rayan
author_sort Dufresne, Yoann
collection PubMed
description 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.
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spelling pubmed-94775202022-09-19 The K-mer File Format: a standardized and compact disk representation of sets of k-mers Dufresne, Yoann Lemane, Teo Marijon, Pierre Peterlongo, Pierre Rahman, Amatur Kokot, Marek Medvedev, Paul Deorowicz, Sebastian Chikhi, Rayan Bioinformatics Applications Note 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. Oxford University Press 2022-07-29 /pmc/articles/PMC9477520/ /pubmed/35904548 http://dx.doi.org/10.1093/bioinformatics/btac528 Text en © The Author(s) 2022. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Dufresne, Yoann
Lemane, Teo
Marijon, Pierre
Peterlongo, Pierre
Rahman, Amatur
Kokot, Marek
Medvedev, Paul
Deorowicz, Sebastian
Chikhi, Rayan
The K-mer File Format: a standardized and compact disk representation of sets of k-mers
title The K-mer File Format: a standardized and compact disk representation of sets of k-mers
title_full The K-mer File Format: a standardized and compact disk representation of sets of k-mers
title_fullStr The K-mer File Format: a standardized and compact disk representation of sets of k-mers
title_full_unstemmed The K-mer File Format: a standardized and compact disk representation of sets of k-mers
title_short The K-mer File Format: a standardized and compact disk representation of sets of k-mers
title_sort k-mer file format: a standardized and compact disk representation of sets of k-mers
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9477520/
https://www.ncbi.nlm.nih.gov/pubmed/35904548
http://dx.doi.org/10.1093/bioinformatics/btac528
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