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

This repository contains processed data tables, analysis scripts, and supporting phylogenetic and plasmid-screening outputs for a benchmarking study evaluating mechanically sheared DNA and Oxford Nanopore Technologies (ONT) basecalling modes, High Accuracy (HAC) and Super Accuracy (SUP), for Salmonella enterica serovar Typhi genomic surveillance. The archive includes: R scripts used to generate the main and supplementary figures QUAST structural summary tables for the 6-plex benchmarking and 24-plex field-validation runs Snippy-derived pairwise SNV distance matrices and SNV occurrence summaries cgMLST allele matrices and allele-distance calculations MUMmer whole-genome alignment summaries comparing hybrid assemblies across runs Gubbins recombination-associated region masking outputs used for Supplementary Figure S5 Newick tree files used for visualization of the technical SNV-based maximum-likelihood phylogeny in iTOL MOB-suite plasmid-screening outputs and curated summaries supporting Supplementary Table S5 These files are provided as supporting materials to ensure transparency and reproducibility of the analyses reported in the manuscript. .