R scripts for genomic benchmarking of Oxford Nanopore HAC and SUP basecalling in Salmonella Typhi

This repository contains R scripts used to generate figures and analyses for a benchmarking study evaluating mechnically sheared DNA with Oxford Nanopore Technologies (ONT) basecalling modes (HAC and SUP) for Salmonella enterica serovar Typhi genomic surveillance. The scripts reproduce all main figures in the manuscript, including QUAST assembly metrics, SNP distance analyses, SNP heatmaps, cgMLST minimum spanning trees, and comparisons between controlled benchmark strains and 24-plex field sequencing runs. Raw sequencing data and genome assemblies are deposited separately in the DDBJ Sequence Read Archive (DRA) and DDBJ Annotated/Assembled Sequences databases. These scripts are provided to ensure transparency and reproducibility of the analyses reported in the manuscript.