Large-scale benchmarking of prokaryotic annotation tools across thousands of species.
- Open access
Bakta and PGAP outperform other tools in annotating diverse prokaryotic genomes, with Bakta excelling in bacteria and PGAP in archaea and challenging assemblies.
- Why it matters: Accurate genome annotation is essential for understanding prokaryotic functions, but systematic evaluations of tools across thousands of species are lacking, hindering optimal tool selection.
- What they did: Analyzing 156,033 genomes using four open-source annotation tools—Prokka, Bakta, EggNOG-mapper, and PGAP—highlighted their strengths and limitations across different genome qualities and taxonomies.
- The result: The study guides users in choosing tools based on genome type and quality, and informs future development, enabling more precise and comprehensive prokaryotic genome annotation.