The GEN-ERA project, which ran from 2020 to 2022, aimed to establish reproducible genomics practices within the Belgian Coordinated Collections of Microorganisms (BCCM). To achieve this goal, a toolbox consisting of 14 Nextflow workflows, each relying on a dedicated Singularity container, was developed. This toolbox addresses the main needs of scientists working in genomics: downloading data, assembling and binning (meta)genomes from short or long reads, as well as performing orthologous inference and maximum-likelihood phylogenomic analyses with bootstrap and jackknife support. Constrained SSU rRNA phylogenies, guided by ribosomal phylogenomics, can also be inferred. In addition, the toolbox includes workflows for average nucleotide identity calculations, GTDB-based taxonomic identification, and metabolic modelling. Since the end of the initial project, GEN-ERA has been actively maintained and has recently been refinanced for a further four-year period (2026–2030), notably to expand and strengthen its functional genomics component.
https://github.com/Lcornet/GENERA

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