Loïc Meunier

The paper introduces the GEN-ERA toolbox, a unified bioinformatics workflow for microbial genomics that enables reproducible phylogenetic and metabolic analyses on bacteria and small eukaryotes.

AMAW automates genome annotation for non-model eukaryotes by integrating MAKER2 and providing a Singularity container for easier deployment.

The paper assesses contamination levels in 440 cyanobacterial genomes using a consensus of six methods, finding over 5% are highly contaminated.