Data and code pertaining to: Decomposition of the S. aureus Pangenome Reveals Evolving Genetic Repertoire Responsible for Adaptation and Virulence

Main Manuscript: Decomposition of the S. aureus Pangenome Reveals Evolving Genetic Repertoire Responsible for Adaptation and VirulenceAll genomes and their metadata were downloaded from BV-BRC, the Bacterial and Viral Bioinformatics Resource Center (https://www.bv-brc.org/) (Olson et al. 2023). All code + metdata files needed to download, clean, process, and enrich data is included. Code needed to generate a pangenome and extract the phylon structrure is also present. Contents: metadata folder with all the different metadata files. enriched_metadata is the final one used for analysis S_aureus (zip): Code files. These are jupyter notebooks that are easy to follow and ordered so you know which one runs in which order. processed (tar.gz): processed output files. These are the processed output files used to generate and inform the analysis conducted. Large: 27GB (ZIPPED) The only think missing are 2 folders: raw and tmp. raw stores raw data which is where most downloads went (redundant since we have procesed reannotated genomes from bakta already present in the processed folder). tmp stores temporary files which are not needed or even useful by themselves. The actual results used to generate the actual analysis are stored in processed, which is included in this repository.