Code for summarizing the data obtained from the workflow published in STAR Protocols.
This framework integrates multiple stages of bioinformatic processing, including sequencing read quality filtering, de novo genome assembly, and functional annotation. It further enables precise genetic characterization through Multi-Locus Sequence Typing (MLST), agr and spa typing, and Staphylococcal Cassette Chromosome mec (SCCmec) classification. Additionally, this workflow provides robust detection of key genomic features, including Antibiotic Resistance Genes (ARGs), Virulence Factors (VFs), plasmids, and prophages.
Sánchez-Osuna M, Erill I, Gasch O, Pich OQ. 2025. Computational protocol for analyzing whole-genome sequencing data from Staphylococcus aureus clinical isolates. STAR Protoc. 2025 Jan 31;6(1):103613. doi: 10.1016/j.xpro.2025.103613
You might also be interested in: Sánchez-Osuna M, Pedrosa M, Bierge P, Gómez-Sánchez I, Alguacil-Guillén M, Espasa M, Erill I, Gasch O, Pich OQ. 2024. Genomic analysis of Staphylococcus aureus isolates from bacteremia reveals genetic features associated with the COVID-19 pandemic. iScience. Jun 28;27(8):110402. doi: 10.1016/j.isci.2024.110402