Infectious Disease Genomic Epidemiology

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Course Objectives

With increasing adoption of Next Generation Sequencing technologies to infectious disease surveillance and outbreak investigations, genomic epidemiology (combining pathogen genomics data with epidemiological investigations to track the spread of infectious diseases) is poised to change the practices of public health and infection controls and provides unprecedented amount of data for pathogen evolution studies.

The CBW has developed a 3-day course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use selected analysis tools. The 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.

Participants will gain practical experience and skills to be able to:

  • Understand next generation sequencing (NGS) platforms as applied to pathogen genomics and metagenomics sequencing
  • Analyze NGS data for pathogen surveillance and outbreak investigations
  • Analyze antimicrobial resistance genes
  • Detect emerging pathogens in metagenomics data
  • Perform phylogeographic analysis
  • Use different visualization tools for genomic epidemiology analysis

Target Audience

Graduates, postgraduates, staff bioinformaticians, laboratory technologists, medical microbiologists and PIs working with or about to embark on analysis of genomic and metagenomics data for epidemiological investigations.

Prerequisites: Basic familiarity with Linux environment and S, R, or Matlab. Must be able to complete and understand the following simple Linux and R tutorials (up to and including “Descriptive Statistics”) before attending:

You will also require your own laptop computer. Minimum requirements: 1024x768 screen resolution, 1.5GHz CPU, 2GB RAM, 10GB free disk space, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements).If you do not have access to your own computer, you may loan one from the CBW. Please contact for more information.

Pre-work and pre-readings can be found at

Course Material