Supplorting files for genomic benchmarking of Oxford Nanopore HAC and SUP basecalling in Salmonella Typhi

This repository contains supporting files associated with a benchmarking study evaluating mechanically sheared DNA and Oxford Nanopore Technologies (ONT) basecalling modes (HAC and SUP) for Salmonella enterica serovar Typhi genomic surveillance. The repository includes analysis scripts used to generate all figures reported in the manuscript, as well as summary whole-genome alignment outputs (dnadiff) used to support the selection of hybrid assemblies as benchmarking references. These materials enable transparency and reproducibility of the comparative assembly, SNP-based, and cgMLST analyses presented in the study. Raw sequencing reads and genome assemblies are deposited separately in the DDBJ Sequence Read Archive (DRA) and the DDBJ/ENA/GenBank Annotated/Assembled Sequences databases, with accession numbers provided in the manuscript and supplementary tables. The files provided here are intended as supporting materials ensure transparency and reproducibility of the analyses reported in the manuscript.