Roary is a tool designed for rapid and large-scale analysis of prokaryote pan genomes, capable of identifying core and accessory genes. It can construct pan genomes from thousands of isolates on a standard desktop computer without compromising accuracy. Roary uses a combination of pre-clustering and all-against-all BLAST comparisons to reduce computational time and memory usage. The tool is implemented in Perl and is freely available under an open-source GPLv3 license. Evaluations against other pan genome tools show that Roary is more accurate, faster, and more memory-efficient, making it suitable for analyzing large datasets.Roary is a tool designed for rapid and large-scale analysis of prokaryote pan genomes, capable of identifying core and accessory genes. It can construct pan genomes from thousands of isolates on a standard desktop computer without compromising accuracy. Roary uses a combination of pre-clustering and all-against-all BLAST comparisons to reduce computational time and memory usage. The tool is implemented in Perl and is freely available under an open-source GPLv3 license. Evaluations against other pan genome tools show that Roary is more accurate, faster, and more memory-efficient, making it suitable for analyzing large datasets.