This repository holds the tabulated data and code behind the paper of the Global Typhoid Genomics Consortium, "Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi" published in Genome Medicine, 2025 (preprint available in BioRxiv). Note that Typhi Mykrobe is not a QC tool. It is recommended that users continue to undertake their own QC on short and long read data.