ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating assemblies

Léonard, Raphaël; Leleu, Marie; Van Vlierberghe, Mick; Cornet, Luc; Kerff, Frédéric; Baurain, Denis

doi:10.7717/peerj.11348

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ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating assemblies

Léonard, Raphaël; Leleu, Marie; Van Vlierberghe, Mick et al.

2021 • In PeerJ, 9, p. 11348

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https://hdl.handle.net/2268/259995

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10.7717/peerj.11348

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Keywords :

Dereplication; Prokaryotes; Genome quality; Genome selection; Alignment-free methods; Phylogenomics; NCBI RefSeq; Singularity; Metagenomics

Abstract :

[en] TQMD is a tool for high-performance computing clusters which downloads, stores and produces lists of dereplicated prokaryotic genomes. It has been developed to counter the ever-growing number of prokaryotic genomes and their uneven taxonomic distribution. It is based on word-based alignment-free methods (k-mers), an iterative single-linkage approach and a divide-and-conquer strategy to remain both efficient and scalable. We studied the performance of TQMD by verifying the influence of its parameters and heuristics on the clustering outcome. We further compared TQMD to two other dereplication tools (dRep and Assembly-Dereplicator). Our results showed that TQMD is primarily optimized to dereplicate at higher taxonomic levels (phylum/class), as opposed to the other dereplication tools, but also works at lower taxonomic levels (species/strain) like the other dereplication tools. TQMD is available from source and as a Singularity container at [https://bitbucket.org/phylogeno/tqmd ].

Disciplines :

Microbiology
Genetics & genetic processes
Biochemistry, biophysics & molecular biology

Author, co-author :

Léonard, Raphaël ; Université de Liège - ULiège > InBioS

Leleu, Marie ; Université de Liège - ULiège > InBioS

Van Vlierberghe, Mick ; Université de Liège - ULiège > InBioS

Cornet, Luc ; Université de Liège - ULiège > Département des sciences de la vie > Phylogénomique des eucaryotes

Kerff, Frédéric ; Université de Liège - ULiège > Département des sciences de la vie > Centre d'ingénierie des protéines

Baurain, Denis ; Université de Liège - ULiège > Département des sciences de la vie > Phylogénomique des eucaryotes

Language :

English

Title :

ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating assemblies

Publication date :

05 May 2021

Journal title :

PeerJ

eISSN :

2167-8359

Publisher :

PeerJ, United States - California

Volume :

Pages :

e11348

Peer reviewed :

Peer Reviewed verified by ORBi

Additional URL :

https://peerj.com/articles/11348/

Funders :

FRIA - Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture
BELSPO - Politique scientifique fédérale
ANR - Agence Nationale de la Recherche
F.R.S.-FNRS - Fonds de la Recherche Scientifique

Available on ORBi :

since 17 May 2021

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