A Practical Bioinformatics Workflow for Routine Analysis of Bacterial WGS Data.

ABSTRACT: The use of whole-genome sequencing (WGS) for bacterial characterisation has increased substantially in the last decade. Its high throughput and decreasing cost have led to significant changes in outbreak investigations and surveillance of a wide variety of microbial pathogens. Despite the innumerable advantages of WGS, several drawbacks concerning data analysis and management, as well as a general lack of standardisation, hinder its integration in routine use. In this work, a bioinformatics workflow for (Illumina) WGS data is presented for bacterial characterisation including genome annotation, species identification, serotype prediction, antimicrobial resistance prediction, virulence-related genes and plasmid replicon detection, core-genome-based or single nucleotide polymorphism (SNP)-ba

SUBMITTER: Atxaerandio-Landa A 

PROVIDER: S-EPMC9781918 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature