Reliable whole-genome genotyping for bacterial surveillance using nanopore sequencing data

Gabriel E. Wagner is a molecular biologist at the Medical University of Graz, specialising in molecular surveillance of circulating pathogens and serological analysis of host immunity, with a focus on epidemiology and diagnostics. His research aims at translating these insights into the development of diagnostic tests and user-friendly tools and workflows for widespread application.

Abstract

Despite recent advances in error rate reduction, Oxford Nanopore Technologies sequencers have until recently lacked the accuracy for reliable fine-scale bacterial genomic analysis. Here, we evaluated recent improvements of tools from Oxford Nanopore Technologies (Dorado basecalling and Medaka polishing) and the Oxford Nanopore cgMLST polisher (Ridom, Germany) on bacterial genotyping.