Large-scale benchmarking of prokaryotic annotation tools across thousands of species.

Bakta outperforms other tools in annotating high-quality bacterial genomes, while PGAP is more effective for archaeal and challenging bacterial assemblies, including metagenome-assembled genomes.

• Why it matters: Accurate genome annotation is essential for understanding prokaryotic functions, but systematic evaluations of annotation tools across diverse genomes are lacking, hindering optimal tool selection.
• What they did: The study analyzed four open-source annotation tools—Prokka, Bakta, EggNOG-mapper, and PGAP—across 156,033 genomes, including Escherichia coli, archaea, bacteria, and metagenome-assembled genomes, to assess their performance.
• The result: Findings reveal tool-specific strengths, with Bakta excelling in high-quality bacterial genomes and PGAP in archaeal and complex bacterial assemblies, guiding users in selecting appropriate annotation solutions based on genome type and quality.