The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.

Gloeobacterales; Cyanobacteria; Singularity containers; culture collections; genomics; metagenomics; nextflow; phylogenomics; phylogeny; workflow; Workflow; Reproducibility of Results; Genome, Microbial; Phylogeny; Genomics/methods; Computational Biology/methods; Medicine (all); Computer Science Applications; Health Informatics

Abstract :

[en] [en] BACKGROUND: Microbial culture collections play a key role in taxonomy by studying the diversity of their strains and providing well-characterized biological material to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms were studied, resulting in the GEN-ERA toolbox. The latter is a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (e.g., yeasts). FINDINGS: This public toolbox allows researchers without a specific training in bioinformatics to perform robust phylogenomic analyses. Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling. TECHNICAL DETAILS: Nextflow workflows are launched by a single command and are available on the GEN-ERA GitHub repository (https://github.com/Lcornet/GENERA). All the workflows are based on Singularity containers to increase reproducibility. TESTING: The toolbox was developed for a diversity of microorganisms, including bacteria and fungi. It was further tested on an empirical dataset of 18 (meta)genomes of early branching Cyanobacteria, providing the most up-to-date phylogenomic analysis of the Gloeobacterales order, the first group to diverge in the evolutionary tree of Cyanobacteria. CONCLUSION: The GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be used by all researchers interested in microbial taxonomy, as exemplified by our case study on Gloeobacterales.

Research center :

InBios - Integrative Biological Sciences - ULiège

Disciplines :

Genetics & genetic processes
Microbiology
Biochemistry, biophysics & molecular biology

Author, co-author :

Cornet, Luc ; Université de Liège - ULiège > Département des sciences de la vie > Phylogénomique des eucaryotes ; BCCM/IHEM, Mycology and Aerobiology, Sciensano, 1050, Brussels, Belgium

Durieu, Benoit ; Université de Liège - ULiège > Integrative Biological Sciences (InBioS)

Baert, Frederik ; BCCM/IHEM, Mycology and Aerobiology, Sciensano, 1050, Brussels, Belgium

D'hooge, Elizabet ; BCCM/IHEM, Mycology and Aerobiology, Sciensano, 1050, Brussels, Belgium

Colignon, David ; Université de Liège - ULiège > Département d'électricité, électronique et informatique (Institut Montefiore) > Applied and Computational Electromagnetics (ACE)

Meunier, Loïc ; Université de Liège - ULiège > Integrative Biological Sciences (InBioS)

Lupo, Valérian ; Université de Liège - ULiège > Département des sciences de la vie > Phylogénomique des eucaryotes

Cleenwerck, Ilse ; BCCM/LMG and Laboratory of Microbiology, Faculty of Sciences, Ghent University, 9000, Ghent, Belgium

Daniel, Heide-Marie ; BCCM/MUCL and Laboratory of Mycology, Earth and Life Institute, Université catholique de Louvain, ELIM 1348, Louvain-la-Neuve, Belgium

Rigouts, Leen ; BCCM/ITM, Mycobacteriology Unit, Institute of Tropical Medicine, 2000, Antwerp, Belgium

More authors (6 more)

Language :

English

Title :

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.

Publication date :

28 December 2022

Journal title :

GigaScience

ISSN :

2047-217X

Publisher :

Oxford University Press, United States

Volume :

Peer reviewed :

Peer Reviewed verified by ORBi

Tags :

CÉCI : Consortium des Équipements de Calcul Intensif

Additional URL :

https://academic.oup.com/gigascience/article-pdf/doi/10.1093/gigascience/giad022/49806243/giad022.pdf

Funders :

BELSPO - Belgian Science Policy Office [BE]
F.R.S.-FNRS - Fonds de la Recherche Scientifique [BE]

Funding text :

This work was supported by a research grant (no. B2/191/P2/BCCM GEN-ERA) financed by the Belgian State—Federal Public Planning Science Policy Office (BELSPO). H.-M.D. is supported by the Belgian Science Policy Office (BELSPO) grant C5/00/BCCM. Computational resources were provided by the Consortium des Équipements de Calcul Intensif (CÉCI), funded by the F.R.S.-Le Fonds National de la Recherche Scientifique (FNRS) (2.5020.11), and through 2 research grants to D.B.: B2/191/P2/BCCM GEN-ERA (Belgian Science Policy Office—BELSPO) and CDR J.0008.20 (F.R.S.-FNRS). A.W. is senior research associate of the FRS-FNRS.

Data Set :

GitHub

Available on ORBi :

since 01 July 2023

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16 (2 by ULiège)

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