This course provided an intensive introduction to the methods used for analysis of whole genome sequencing (WGS) data and its application to infectious disease epidemiology. Students learned bioinformatics approaches to WGS analysis through a combination of lectures and hands-on workshops. Topics included how to perform de novo versus reference-based assembly, how to identify (‘call’) single nucleotide polymorphisms, and creating/interpreting phylogenetic trees. Emphasis was placed on applications of WGS to outbreak investigation, study design issues and minimizing bias in...