Benchmarking Oxford Nanopore sequencing workflows for Salmonella enterica serovar Typhi genomic surveillance

This project generates whole-genome sequencing data to benchmark Oxford Nanopore Technologies (ONT) workflows for Salmonella enterica serovar Typhi genomic surveillance. The study evaluates the impact of mechanical DNA shearing and basecalling modes (High Accuracy and Super Accuracy) on sequencing performance, assembly quality, and downstream genomic analyses. Sequencing data were produced from three benchmark S. Typhi strains under controlled multiplexing conditions, as well as from clinical isolates obtained through a sentinel hospital surveillance programme in Manila, Philippines, to assess performance under higher multiplex and field-like conditions. Both ONT long-read data and Illumina short-read data were generated, and strain-specific hybrid assemblies were constructed to serve as references for benchmarking. The resulting datasets support comparative analyses of read quality, genome assembly metrics, single-nucleotide variation concordance, cgMLST resolution, and genotyping and antimicrobial resistance prediction. These data are intended to support methodological validation and reproducibility of ONT-based workflows for bacterial genomic surveillance and will also serve as a resource for future method development and comparative studies.