Curated ecoli datasets for prokaryotic pangenomics

Curated E. coli GFF dataset – A quality-controlled set of genome assemblies in GFF3 format, standardized for direct PGAP2 input. These files have consistent annotation structure to support accurate gene clustering and pan-genome construction.gold_EC_all.csv – A comprehensive clustering result that includes both orthologous and paralogous genes.gold_EC_unpara.csv – A refined clustering result containing only orthologous genes (paralogues excluded).Other intermediate steps and scripts are available at: https://github.com/bucongfan/PGAP2_benchmark. For using the latest version of our software or for any inquiries, please visit: https://github.com/bucongfan/PGAP2