{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/whole-genome-single-nucleotide-polymorphism","title":"Whole genome single nucleotide polymorphism genotyping of Staphylococcus aureus","arxiv_id":"1810.13027","date":"2018-10-30","proceeding":null,"authors":[],"abstract":"Next-generation sequencing technology enables routine detection of bacterial\npathogens for clinical diagnostics and genetic research. Whole genome\nsequencing has been of importance in the epidemiologic analysis of bacterial\npathogens. However, few whole genome sequencing-based genotyping pipelines are\navailable for practical applications. Here, we present the whole genome\nsequencing-based single nucleotide polymorphism (SNP) genotyping method and\napply to the evolutionary analysis of methicillin-resistant Staphylococcus\naureus. The SNP genotyping method calls genome variants using next-generation\nsequencing reads of whole genomes and calculates the pair-wise Jaccard\ndistances of the genome variants. The method may reveal the high-resolution\nwhole genome SNP profiles and the structural variants of different isolates of\nmethicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus\n(MSSA) strains. The phylogenetic analysis of whole genomes and particular\nregions may monitor and track the evolution and the transmission dynamic of\nbacterial pathogens. The computer programs of the whole genome sequencing-based\nSNP genotyping method are available to the public at\nhttps://github.com/cyinbox/NGS.","url_abs":"http://arxiv.org/abs/1810.13027v1","url_pdf":"http://arxiv.org/pdf/1810.13027v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"whole-genome-single-nucleotide-polymorphism","repo_url":"https://github.com/cyinbox/NGS","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}