Infectious Disease Genomic Epidemiology 2023


The course schedule can be found here

Meet your faculty here

Pre-Workshop Materials

Pre-work including programs to install can be found here

AWS Module

Please follow the instructions to log into your AWS instance.
The content for our AWS/Unix review session on April 17th can be found here.
The schedule for this session can be found here.

Class Photo

Infectious Disease Genomic Epidemiology Class of 2023

Day 1

Virtual Welcome

Nia Hughes

Module 1: Introduction to Genomic Epidemiology

William Hsiao

Module 1 Lecture Recording
Module 1 Lecture Slides

Module 2: Phylogenetic Analysis

Fiona Brinkman

Module 2 Lecture Recording
Module 2 Lecture Slides

AWS Setup

Zhibin Lu

Slides (pdf)

You can find the instructions here.

Module 3: Data Curation and Data Sharing

Emma Griffiths

Module 3 Lecture Recording
Module 3 Lecture Slides


Module 3 Lab

Day 2

Module 4: Viral Pathogen Genomic Analysis - Single Nucleotide Variants

Jared Simpson

Module 4 Lecture Recording
Module 4 Lecture Slides


Module 4 Lab

Module 5: Bacterial Pathogen Genomic Analysis

Ed Taboada

Module 5 Lecture Recording
Module 5 Lecture Slides


Module 5 Lab Setup
Module 5 Lab

Day 3

Module 6: Antimicrobial Resistant Gene (AMR) Analysis

Andrew McArthur

Module 6 Lecture Recording
Module 6 Lecture Slides


Module 6 Lab

Module 7: Phylodynamics and Transmission Dynamics

Finlay Maguire

Module 7 Lecture Recording
Module 7 Lecture Slides


Module 7 Lab

Day 4

Module 8: Emerging Pathogen Detection and Identification

Aaron Petkau

Module 8 Lecture Recording
Module 8 Lecture Slides


Module 8 Lab Module 8 Lab Slides

Keynote Lecture | Follow That Virus!: Genomics Leading the Way

Dr. Samira Mubareka

Keynote Lecture Recording
Keynote Lecture Slides

Module 9: Mobile Genetic Elements and Environmental Microbiome

Gary Van Domselaar

Module 9 Lecture Recording
Module 9 Lecture Slides


Module 9 Lab

Post-Workshop Materials


Note that some of these files are quite large. If you have issues downloading them, contact us at


We have made our AWS AMI (Amazon Machine Image) publicly available. To launch your own instance, follow the instructions provided by Amazon on how to launch an EC2 instance from a custom Amazon Machine Image. Please note that you will need an AWS account to proceed, and that you will need to upload the CourseData files yourself.

Here are the details of the AMI:

  • AWS Region: us-east-1 (N. Virgina)
  • AMI type: public image
  • AMI name: CBW_230416
  • AMI ID: ami-0b905fa1d1d233a17

If you want to create and activate a new AWS account, please follow the instructions provided by Amazon.


For information on installing the necessary tools, please visit

Tools Installation