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

This repository contains processed data tables and analysis scripts supporting 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 archive includes: R scripts used to generate all main and supplementary figures QUAST structural summary tables for 6-plex and 24-plex runs SNIPPY-derived pairwise SNV distance matrices and SNP occurrence summaries cgMLST allele matrices and allele distance calculations MUMmer whole-genome alignment summaries comparing hybrid assemblies across runs newick.txt file for technical SNV-Maximum Likelihood tree developed in iTOL The files provided here are intended as supporting materials ensure transparency and reproducibility of the analyses reported in the manuscript.