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 RedOak: a reference-free and alignment-free structure for indexing a collection of similar genomes Clément Agret 6ae57246ee27ff2ed4fff3d53e070d2e lirmm.fr 1211256 1865818-1211256 https://orcid.org/0000-0002-7404-7253 https://www.idref.fr/250366339 Annie Chateau 4c0e4613d8ee10ee4e1c98180000b379 lirmm.fr annie-chateau 173624 44100-173624 https://orcid.org/0000-0003-4760-8171 https://www.idref.fr/227798856 Gaëtan Droc e92d42b1804a1f1a5d30d17d92911a37 cirad.fr 1213825 446935-1213825 https://orcid.org/0000-0003-1849-1269 https://www.idref.fr/250355345 https://viaf.org/viaf/168160789859202682279 Gautier Sarah e71b7a5c0f11d6867d9e84362c5403da inra.fr gsarah 1206554 904889-1206554 https://orcid.org/0000-0001-5179-972X Alban Mancheron ce3caf574b0e2c250ca57256ca29269e inria.fr alban-mancheron 6019 17693-6019 https://orcid.org/0000-0001-9249-7592 https://www.idref.fr/111581362 Manuel Ruiz f4b91ca332ea2d8fb35219fde774db2f cirad.fr 1203055 446941-1203055 https://orcid.org/0000-0001-8153-276X https://www.idref.fr/069152543 Alban Mancheron 6118fb5e940d1b1f5500c967a8327983 lirmm.fr 2021-01-21 11:06:00 2025-07-17 03:06:55 2021-01-21 12:45:24 2021-01-21 2021-01-21 contributor Alban Mancheron 6118fb5e940d1b1f5500c967a8327983 lirmm.fr CCSD lirmm-03117453 https://hal-lirmm.ccsd.cnrs.fr/lirmm-03117453 agret:lirmm-03117453 2021 2021 HAL Authorization CIRAD - Centre de coopération internationale en recherche agronomique pour le développement CNRS - Centre national de la recherche scientifique Méthodes et Algorithmes pour la Bioinformatique Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier Archive ouverte en agrobiosciences Mathématiques, Informatique, Physique et Systèmes Biologie-AgroSciences Université de Montpellier Institut Agro Montpellier Institut National de Recherche en Agriculture, Alimentation et Environnement INRAE Occitanie Montpellier ANR AGAP Université de Montpellier (2015-2021) Institut Agro Département BAP INRAE RedOak: a reference-free and alignment-free structure for indexing a collection of similar genomes Clément Agret 6ae57246ee27ff2ed4fff3d53e070d2e lirmm.fr 1211256 1865818-1211256 https://orcid.org/0000-0002-7404-7253 https://www.idref.fr/250366339 Annie Chateau 4c0e4613d8ee10ee4e1c98180000b379 lirmm.fr annie-chateau 173624 44100-173624 https://orcid.org/0000-0003-4760-8171 https://www.idref.fr/227798856 Gaëtan Droc e92d42b1804a1f1a5d30d17d92911a37 cirad.fr 1213825 446935-1213825 https://orcid.org/0000-0003-1849-1269 https://www.idref.fr/250355345 https://viaf.org/viaf/168160789859202682279 Gautier Sarah e71b7a5c0f11d6867d9e84362c5403da inra.fr gsarah 1206554 904889-1206554 https://orcid.org/0000-0001-5179-972X Alban Mancheron ce3caf574b0e2c250ca57256ca29269e inria.fr alban-mancheron 6019 17693-6019 https://orcid.org/0000-0001-9249-7592 https://www.idref.fr/111581362 Manuel Ruiz f4b91ca332ea2d8fb35219fde774db2f cirad.fr 1203055 446941-1203055 https://orcid.org/0000-0001-8153-276X https://www.idref.fr/069152543 10.1101/2020.12.19.423583 English Data structure Similar genomes Pan-genomes k-mer Computer Science [cs]/Data Structures and Algorithms [cs.DS] Preprints, Working Papers, ... Preprints, Working Papers, ... Preprints, Working Papers, ...

Background: As the cost of DNA sequencing decreases, high-throughput sequencing technologies become increasingly accessible to many laboratories. Consequently, new issues emerge that require new algorithms, including tools for indexing and compressing hundred to thousands of complete genomes.Results: This paper presents RedOak, a reference-free and alignment-free software package that allows for the indexing of a large collection of similar genomes. RedOak can also be applied to reads from unassembled genomes, and it provides a nucleotide sequence query function. This software is based on a k-mer approach and has been developed to be heavily parallelized and distributed on several nodes of a cluster. The source code of our RedOak algorithm is available at https://gitlab.info-ufr.univ-montp2.fr/DoccY/RedOak.Conclusions: RedOak may be really useful for biologists and bioinformaticians expecting to extract information from large sequence datasets.

 Méthodes et Algorithmes pour la Bioinformatique MAB 2021-12-31
LIRMM, 161 rue Ada, 34000 Montpellier
https://www.lirmm.fr/equipes/MAB/ 0000000404458705 201119637B https://ror.org/02w4exq36 Amélioration génétique et adaptation des plantes méditerranéennes et tropicales UMR AGAP 2020-01-01 2021-12-31
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https://www.lirmm.fr 0000000120970141 https://ror.org/051escj72 Université de Montpellier UM 2021-12-31
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http://www.cirad.fr https://ror.org/003vg9w96 Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement INRAE 2020-01-01
261038990 https://ror.org/03rnk6m14 Institut Agro - Montpellier SupAgro 2020-01-01 2021-12-31
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https://www.institut-agro-montpellier.fr/ 260373249 https://ror.org/01dkyve95 Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement Institut Agro 2020-01-01
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