Due to Next-Generation Sequence technologies, sequencing of bacterial genomes is no longer one of the main bottlenecks in bacterial research. Therefore, the number of new genomes deposited in public data bases continues to increase at an accelerating rate. Among these new genomes, there are several from the same species, which were generated for pangenomic studies. A pangenomic study allows the investigation of a strain’s phenotype differences based on genotype differences. In order to achieve its goals, besides having good assembly quality, it is also fundamental to guarantee good functional genome annotation among the different strains. This process will facilitate the identification of genes presented in all, in a few, or in a unique strain.

In order to address these issues, we present PANNOTATOR, a web-based, automated pipeline for the annotation of closely related genomes well suited for pangenome studies. This tool was developed to reduce the manual work needed to generate reports and corrections of various genome strains. One of the main features of this tool is the fast and automatic generation of an annotation based on a gold standard manual annotation.