Comparative Genomics of ESKAPE Pathogens: Integrating Pan-genome Architecture, Antimicrobial Resistance, and Virulence Factor Repertoires — Full Dataset

Complete input-to-output dataset for the comparative genomics analysis of 120 ESKAPE pathogen genomes (20 strains × 6 species: Acinetobacter, Enterobacter, Enterococcus, Klebsiella, Pseudomonas, Staphylococcus). This archive includes: - Raw genome assemblies (120 .fna files) - Prokka annotations for all 120 strains - Roary pan-genome outputs for all 6 species - CheckM2 quality control reports - AMRFinderPlus raw resistance profiling outputs - DIAMOND virulence screening outputs against VFDB - All analysis result tables and summary statistics - Python analysis pipeline scripts (scripts 01–09) - Metadata and authorship information The corresponding analysis pipeline and summary tables are available on GitHub (see Related Works). Version 2 includes revised phylogenetic analyses, Benjamini–Hochberg FDR-corrected statistical outputs, updated Fisher enrichment analyses, and corresponding revised analysis scripts prepared for the revised manuscript.