RedOak

RedOak stand for Reference-free[d] Optimized approach by k-mers, RedOak is an alignment-free and reference-free software which allows to index a large collection of similar genomes. RedOak can also be applied to reads from unassembled genomes.

Keywords

indexation k-mers pangenomics comparative genomics genomic variations

Domains

Bioinformatics [q-bio.QM]

Cites lirmm-03920648 Journal article 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⟩

Cathy Tuchming : Connect in order to contact the contributor

https://hal-lirmm.ccsd.cnrs.fr/lirmm-03925385

Submitted on : Thursday, January 5, 2023-3:58:12 PM

Last modification on : Friday, May 31, 2024-6:32:03 PM

Dates and versions

lirmm-03925385 , version 1 (05-01-2023)

Identifiers

HAL Id : lirmm-03925385 , version 1
SWHID : swh:1:dir:b0ab791cdb79f7adebb98549a2546e0b070b8237;origin=https://gite.lirmm.fr/doccy/RedOak;visit=swh:1:snp:ee2f64fb510a243f2e7ac0875b80c782c4bc0351;anchor=swh:1:rev:c875c2a7a70de544e900ffdbc0fecc11c8ecd469

version : v0.1.4
Software License : CeCILL Free Software License Agreement v2.1
Programming Language : C++
Code Repository : https://gite.lirmm.fr/doccy/RedOak
Platform/OS : GNU/Linux

Cite

Clément Agret, Alban Mancheron, Gautier Sarah. RedOak. 2017, ⟨swh:1:dir:b0ab791cdb79f7adebb98549a2546e0b070b8237;origin=https://gite.lirmm.fr/doccy/RedOak;visit=swh:1:snp:ee2f64fb510a243f2e7ac0875b80c782c4bc0351;anchor=swh:1:rev:c875c2a7a70de544e900ffdbc0fecc11c8ecd469⟩. ⟨lirmm-03925385⟩

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