Code for summarizing the data obtained from the workflow under review 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.
(Currently under review in STAR Protocols)
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