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 and Pierre Becker
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).
https://doi.org/10.1093/gigascience/giad022

• 2023
• Genomic Workflows