Fig. 2

Annotation tool comparison using E. coli genomes. The number of entries in the databases (a) used by the different annotation tools showed that MicrobeAnnotator has the highest number of database entries compared to other tools. The annotation of 100 E. coli genomes showed that MicrobeAnnotator and DRAM, being the most comprehensive tools, required more than 2 h to annotate each genome using 10 threads (b). Faster tools such as Prokka compared with the light version of MicrobeAnnotator, requiring only minutes to perform the annotations. The more extensive databases used by MicrobeAnnotator resulted in higher RAM usage in par to that required by DRAM (c). Finally, the percentage of proteins classified as annotated (A), hypothetical (H), and unannotated (U) showed that MicrobeAnnotator could annotate more than 90% of proteins for well-represented genomes. In comparison, the light version still annotates ~ 80% of the proteins, suggesting it is an efficient annotation option for microorganisms with good representation in the databases (d). MA MicrobeAnnotator, MAL MicrobeAnnotator Light, EGG EggNOG-Mapper, IPS InterProScan, PROK Prokka