@article{01H14FM0VSDNF5ZAXCAA6G7H96,
  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.}},
  articleno    = {{giad022}},
  author       = {{Cornet, Luc and Durieu, Benoit and Baert, Frederik and D'hooge, Elizabet and Colignon, David and Meunier, Loic and Lupo, Valérian and Cleenwerck, Ilse and Daniel, Heide-Marie and Rigouts, Leen and Sirjacobs, Damien and Declerck, Stéphane and Vandamme, Peter and Wilmotte, Annick and Baurain, Denis and Becker, Pierre}},
  issn         = {{2047-217X}},
  journal      = {{GIGASCIENCE}},
  keywords     = {{Computer Science Applications,Health Informatics,workflow,genomics,metagenomics,phylogeny,phylogenomics,culture collections,nextflow,Singularity containers,Gloeobacterales,Cyanobacteria}},
  language     = {{eng}},
  pages        = {{giad022:1--giad022:10}},
  title        = {{The GEN-ERA toolbox : unified and reproducible workflows for research in microbial genomics}},
  url          = {{http://doi.org/10.1093/gigascience/giad022}},
  volume       = {{12}},
  year         = {{2023}},
}

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