Reproducible Pan-genome Framework for Staphylococcus aureus Integrating Environmental and RefSeq Genomes

This project provides the data resources and computational workflows used for the pan-genome analysis of Staphylococcus aureus, integrating a newly sequenced environmental isolate with publicly available complete genomes from NCBI RefSeq. The repository contains scripts for genome retrieval, uniform re-annotation, pan-genome inference, and downstream gene-content analyses, as well as frozen genome inclusion lists and configuration files to ensure full reproducibility. The workflow enables standardized reconstruction of core and accessory genome structure, assessment of gene presence–absence variation, and investigation of population-level genomic stratification. All materials are shared to support transparency, methodological validation, and reuse in comparative microbial genomics studies.