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Updated: Nov 5, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

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

Raphaël R Léonard^1,2, Marie Leleu^2,3, Mick Van Vlierberghe²

¹InBioS - Centre d'Ingénierie des Protéines, Université de Liège, Liège, Belgium.

|May 17, 2021

Summary

This summary is machine-generated.

TQMD is a new tool for prokaryotic genome dereplication on high-performance clusters. It efficiently handles large datasets using k-mers and is optimized for higher taxonomic levels.

Keywords:

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

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Last Updated: Nov 5, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

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Published on: August 20, 2021

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Published on: May 9, 2017

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

The number of available prokaryotic genomes is rapidly increasing.
Uneven taxonomic distribution poses challenges for genome analysis and dereplication.
Existing tools may not efficiently handle large-scale prokaryotic genome datasets.

Purpose of the Study:

To introduce TQMD, a novel tool for efficient prokaryotic genome dereplication.
To evaluate the performance and scalability of TQMD.
To compare TQMD with existing dereplication tools.

Main Methods:

TQMD utilizes word-based alignment-free methods (k-mers).
It employs an iterative single-linkage approach and a divide-and-conquer strategy.
Performance was assessed by parameter influence and comparison with dRep and Assembly-Dereplicator.

Main Results:

TQMD demonstrates efficiency and scalability for prokaryotic genome dereplication.
The tool is optimized for dereplication at higher taxonomic levels (phylum/class).
TQMD also performs dereplication at lower taxonomic levels (species/strain).

Conclusions:

TQMD offers an efficient and scalable solution for prokaryotic genome dereplication.
Its optimization for higher taxonomic levels distinguishes it from other tools.
TQMD is a valuable addition to the bioinformatics toolkit for managing large genome datasets.