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

  1. Luc Cornet
  2. Benoit Durieu
  3. Frederik Baert
  4. Elizabet D’hooge
  5. David Colignon
  6. Loic Meunier
  7. Valérian Lupo
  8. Ilse Cleenwerck
  9. Heide-Marie Daniel
  10. Leen Rigouts
  11. Damien Sirjacobs
  12. Stéphane Declerck
  13. Peter Vandamme
  14. Annick Wilmotte
  15. Denis Baurain
  16. Pierre Becker
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Abstract

Background

Microbial culture collections play a key role in taxonomy by studying the diversity of their accessions and providing well characterized strains 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 (BCCM) were studied, resulting in the GEN-ERA toolbox. The latter is a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (i.e. yeasts).

Findings

This public toolbox allows researchers without a specific training in bioinformatics to perform robust phylogenetic 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 (<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/Lcornet/GENERA">https://github.com/Lcornet/GENERA</ext-link>). 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 theGloeobacteralesorder, 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 useful for other applications, as shown by our case study onGloeobacterales.

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