Sequencing data, assemblies and analysis scripts for validated small Col-like accessory elements in a near-clonal same-host stool–blood Salmonella pair

It contains the raw sequencing data, genome assemblies and analysis scripts used in the study. The dataset includes Illumina sequencing data and draft assemblies for the Salmonella isolates analyzed in the work, Oxford Nanopore sequencing data and a closed assembly for XY1, and scripts used for core SNP filtering, accessory-element analysis, read-depth assessment, junction-read analysis and public-background screening.

These files support reproducibility of the genomic analyses reported in the manuscript.