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

PeerJ

article

Raphaël R. Léonard¹  Marie Leleu²  Mick Van Vlierberghe²  Luc Cornet²  Frédéric Kerff¹  Denis Baurain² 

[1] InBioS – Centre d’Ingénierie des Protéines, Université de Liège;InBioS –PhytoSYSTEMS, Eukaryotic Phylogenomics, Université de Liège;UGSF –Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille/CNRS;Mycology and Aerobiology

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

DOI  :  10.7717/peerj.11348

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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 ].

【 授权许可】

CC BY