Bioinformatics for public health microbiologists: Module 1 dataset (South African Salmonella)

Module 1 (WGS) dataset (paired-end Illumina reads of Salmonella enterica strains isolated from animals and animal products in South Africa)

module1_dataset_ZAsalmonella.tar.gz: raw Illumina paired-end reads

trimmed_reads.tar.gz: trimmed Illumina paired-end reads (i.e., trimmed via fastp v0.23.4)

contigs.tar.gz: assembled genomes (i.e., trimmed reads assembled into contigs using SKESA v2.5.1)

prokka.tar.gz: whole-genome annotation results (i.e., produced via Prokka v1.14.6)

enterobase_salmonella.tar.gz: publicly available assembled genomes (downloaded via Enterobase; https://enterobase.warwick.ac.uk/, accessed 1 June 2024)

snippy_input.tsv: input file used for Snippy (https://github.com/tseemann/snippy)

snippy_final.tar.gz: output files produced by Snippy (https://github.com/tseemann/snippy), Gubbins (https://github.com/nickjcroucher/gubbins), and SNP-sites (https://github.com/sanger-pathogens/snp-sites)