typhoidgenomics/genotyphi

Holt, KEORCID logo, Dyson, ZAORCID logo, Hawkey, J and flashton2003 (2024). typhoidgenomics/genotyphi. [Dataset]. Zenodo. https://doi.org/10.5281/zenodo.4707613
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This repository houses the GenoTyphi genotyping scheme for Salmonella Typhi. It also describes how to call genotypes, AMR and plasmid markers from Typhi whole-genome sequence reads using Mykrobe ('Typhi Mykrobe') and provides links to alternative tools for calling genotypes from reads or assemblies.

Keywords

Antimicrobial resistance, Pathogen genotyping, Salmonella Typhi, typhoid fever, Whole-genome sequencing

Item Type Dataset
Capture method Other
Date 30 September 2024
Language(s) of written materials English
Creator(s) Holt, KEORCID logo, Dyson, ZAORCID logo, Hawkey, J and flashton2003
LSHTM Faculty/Department Faculty of Infectious and Tropical Diseases > Dept of Immunology and Infection (-2019)
Participating Institutions London School of Hygiene & Tropical Medicine, London, United Kingdom
Date Deposited 07 Feb 2022 10:05
Last Modified 03 Oct 2024 09:49
Publisher Zenodo

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