#Bakta → high-quality bacterial isolates / described coding density
#PGAP → Archaea, MAGs, fragmented/problematic genomes, GO coverage
#EggNOG-mapper → functional richness
#Prokka → fast and lightweight, but more limited

Functional annotation adds another layer. For Gene Ontology annotation:
#PGAP: higher GO coverage across diverse Bacteria and Archaea
#EggNOG: greater GO richness per annotated gene

Jundzill et al. benchmarked four widely used open-source annotation tools: #Prokka #Bakta #EggNOG #PGAP; over 156,033 genomes, including bacterial and archaeal genomes, E. coli strains, MAGs and genomes with simulated frameshifts.

The main message? There is no universal winner.