Microbial genomics is transforming many domains, including epidemiology, agriculture, and global ecology, with high-throughput DNA sequencing now being used to examine hundreds to thousands of microbial genomes at a time. Effective analysis of genomes involves several steps including sequence assembly, annotation of functional genes and mobile genetic elements, pan-genome analysis, and phylogenomics. Each of these steps requires careful attention to quality control, software and parameter choices, interpretation of outputs, and visualization. The goal of the Microbial Genomics (MIG) workshop is to provide students with theoretical and hands-on experience into key steps of this analysis pipeline to support small- and large-scale analysis of genomic data. Course tutorials are designed as self-contained units that include example data and detailed instructions for installation of all required bioinformatics tools or access to publicly available web applications. Tutorial datasets will be One Health-focused but the techniques will be applicable to analysis of genomes collected from other habitats. Microbial Genomics is immediately followed by a three-day CBW course that applies the skills gained  in this workshop to infectious disease epidemiology (Part 2 – Infectious Disease Genomic Epidemiology). Microbial Genomics and Infectious Disease Genomic Epidemiology can be taken together or separately. The Microbial Genomics workshop focuses on foundational skills (no prior bioinformatics experience required) and is not specific to pathogens.