ArticleGigaScience2022
The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.
Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Exploring thylakoid emergence: evolution of membrane biogenesis and photosystem II assembly in early-diverging cyanobacteria.The New phytologist · 2026Article
- Horizontal Gene Transfers Underpin Ribose Heterotrophy and Central Carbon Metabolism Remodeling in Gloeobacteraceae.Genome biology and evolution · 2026Article
- Exploring Thylakoid Emergence: Evolution of Membrane Biogenesis and Photosystem II assembly in early-diverging Cyanobacteria.bioRxiv : the preprint server for biology · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Taxonomic description of cyanobacteria from extreme habitats through genome-based classification.Frontiers in microbiology · 2026Article
- Fate and Removal of Antibiotics and Antibiotic Resistance Genes in a Rural Wastewater Treatment Plant: A Microbial Perspective of Nature-Based Versus Advanced Technologies.Microorganisms · 2025Article
- Article
- Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG.F1000Research · 2024Article
- TADA: taxonomy-aware dataset aggregator.Bioinformatics (Oxford, England) · 2023Article
- The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.GigaScience · 2022Article
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Authors and funding
16 authors.
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Abstract
backgroundMicrobial 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).
findingsThis 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.
conclusionThe 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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