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

Luc Cornet; Benoit Durieu; Frederik Baert; Elizabet D'hooge; David Colignon; Loic Meunier; Valérian Lupo; Ilse Cleenwerck; Heide-Marie Daniel; Leen Rigouts; Damien Sirjacobs; Stéphane Declerck; Peter Vandamme; Annick Wilmotte; Denis Baurain; Pierre Becker

doi:10.1093/gigascience/giad022

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

Luc Cornet, Benoit Durieu, Frederik Baert, Elizabet D'hooge, David Colignon, Loic Meunier, Valérian Lupo, Ilse Cleenwerck, Heide-Marie Daniel, Leen Rigouts, Damien Sirjacobs, Stéphane Declerck, Peter Vandamme, Annick Wilmotte, Denis Baurain, Pierre Becker

Mycobacteriology

Research output: Contribution to journal › A1: Web of Science-article › peer-review

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Abstract

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.

Original language	English
Journal	GigaScience
Volume	12
Pages (from-to)	giad022
ISSN	2047-217X
DOIs	https://doi.org/10.1093/gigascience/giad022
Publication status	Published - 2022

Keywords

Workflow
Reproducibility of Results
Genomics/methods
Computational Biology/methods
Genome, Microbial
Phylogeny

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10.1093/gigascience/giad022Licence: CC BY

2023gigagiad022Final published version, 896 KBLicence: CC BY

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Cornet, L., Durieu, B., Baert, F., D'hooge, E., Colignon, D., Meunier, L., Lupo, V., Cleenwerck, I., Daniel, H.-M., Rigouts, L., Sirjacobs, D., Declerck, S., Vandamme, P., Wilmotte, A., Baurain, D., & Becker, P. (2022). The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics. GigaScience, 12, giad022. https://doi.org/10.1093/gigascience/giad022

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title = "The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics",

abstract = "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.",

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author = "Luc Cornet and Benoit Durieu and Frederik Baert and Elizabet D'hooge and David Colignon and Loic Meunier and Val{\'e}rian Lupo and Ilse Cleenwerck and Heide-Marie Daniel and Leen Rigouts and Damien Sirjacobs and St{\'e}phane Declerck and Peter Vandamme and Annick Wilmotte and Denis Baurain and Pierre Becker",

note = "FTX; (CC BY 4.0); {\textcopyright} The Author(s) 2023. Published by Oxford University Press GigaScience.",

year = "2022",

doi = "10.1093/gigascience/giad022",

language = "English",

volume = "12",

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Cornet, L, Durieu, B, Baert, F, D'hooge, E, Colignon, D, Meunier, L, Lupo, V, Cleenwerck, I, Daniel, H-M, Rigouts, L, Sirjacobs, D, Declerck, S, Vandamme, P, Wilmotte, A, Baurain, D & Becker, P 2022, 'The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics', GigaScience, vol. 12, pp. giad022. https://doi.org/10.1093/gigascience/giad022

TY - JOUR

T1 - The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics

AU - Cornet, Luc

AU - Durieu, Benoit

AU - Baert, Frederik

AU - D'hooge, Elizabet

AU - Colignon, David

AU - Meunier, Loic

AU - Lupo, Valérian

AU - Cleenwerck, Ilse

AU - Daniel, Heide-Marie

AU - Rigouts, Leen

AU - Sirjacobs, Damien

AU - Declerck, Stéphane

AU - Vandamme, Peter

AU - Wilmotte, Annick

AU - Baurain, Denis

AU - Becker, Pierre

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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.

KW - Workflow

KW - Reproducibility of Results

KW - Genomics/methods

KW - Computational Biology/methods

KW - Genome, Microbial

KW - Phylogeny

U2 - 10.1093/gigascience/giad022

DO - 10.1093/gigascience/giad022

M3 - A1: Web of Science-article

C2 - 37036103

SN - 2047-217X

VL - 12

SP - giad022

JO - GigaScience

JF - GigaScience

ER -

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

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Keywords

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