RedOak: a reference-free and alignment-free structure for indexing a collection of similar genomes

Here we present 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. Our method is about the analysis of complete genomes from the 3000 rice genomes sequencing project, but our indexing structure is generic enough to be used in similar projects. 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 RedOak.

Domaines

Algorithme et structure de données [cs.DS] Bio-informatique [q-bio.QM]

Fichier principal

joss.04363.pdf (249.9 Ko)

Origine : Fichiers produits par l'(les) auteur(s)

Cathy Tuchming : Connectez-vous pour contacter le contributeur

https://hal-lirmm.ccsd.cnrs.fr/lirmm-03920648

Soumis le : mercredi 11 octobre 2023-09:57:25

Dernière modification le : jeudi 7 mars 2024-14:26:04

Archivage à long terme le : vendredi 12 janvier 2024-18:25:57

Dates et versions

lirmm-03920648 , version 1 (11-10-2023)

Licence

Paternité

Identifiants

HAL Id : lirmm-03920648 , version 1
DOI : 10.21105/joss.04363

Citer

Clément Agret, Annie Chateau, Gaetan Droc, Gautier Sarah, Manuel Ruiz, et al.. RedOak: a reference-free and alignment-free structure for indexing a collection of similar genomes. Journal of Open Source Software, 2022, 7 (80), pp.4363. ⟨10.21105/joss.04363⟩. ⟨lirmm-03920648⟩

Exporter

BibTeX XML-TEI Dublin Core DC Terms EndNote DataCite

Collections

CIRAD CNRS INRIA MAB LIRMM CRISTAL CRISTAL-BONSAI UNIV-MONTPELLIER UNIV-LILLE INSTITUT-AGRO-MONTPELLIER INRAE INRAEOCCITANIEMONTPELLIER AGAP BIOLOGIE_ET_AMELIORATION_DES_PLANTES

64 Consultations

37 Téléchargements