Evalaution of genotyping for ONT sequencing

This study explores the use of Oxford Nanopore Technologies (ONT) for outbreak analysis of four low-mutation-rate bacterial pathogens: Bacillus anthracis, Brucella melitensis, Brucella suis, and Francisella tularensis. 34 strains from previously published Illumina-based outbreaks were selected to compare ONT and Illumina sequencing for SNP detection and cgMLST. Three SNP calling tools—PACU, Clair3, and Snippy—were tested using Illumina-based Snippy calls as the reference, and cgMLST was used to assess genotyping resolution across platforms.