Infectious Disease Genomic Epidemiology 2024
Welcome
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 May 10th can be found here.
The schedule for this session can be found here.
Class Photo
Infectious Disease Genomic Epidemiology Class of 2024
Day 1
Virtual Welcome
Nia Hughes
AWS Setup
Zhibin Lu
You can find the instructions here.
Module 1: Introduction to Genomic Epidemiology
William Hsiao
Module 1 Lecture Recording
Module 1 Lecture Slides
Module 2: De Novo Genome Assembly and Annotation
Gary Van Domselaar
Module 2 Lecture Recording
Module 2 Lecture Slides
Lab
Integrative Assignment
| Integrative Assignment 1 | Answer Key |
| Integrative Assignment 2 | Answer Key |
Day 2
Module 3: Data Curation and Data Sharing
Emma Griffiths
Module 3 Lecture Recording
Module 3 Lecture Slides
Lab
Module 3 Lab
Module 3 Lab Instructions
Module 4: Phylogenetic Analysis
Fiona Brinkman
Module 4 Lecture Recording
Module 4 Lecture Slides
Day 3
Module 5: Viral Pathogen Genomic Analysis - Single Nucleotide Variants
Jared Simpson
Module 5 Lecture Recording
Module 5 Lecture Slides
Lab
Module 6: Bacterial Pathogen Genomic Analysis - Genome-based Subtyping
Ed Taboada
Module 6 Lecture Recording
Module 6 Lecture Slides
Lab
Day 4
Module 7: Antimicrobial Resistant Gene (AMR) Analysis
Andrew McArthur
Module 7 Lecture Recording
Module 7 Lecture Slides
Lab
Module 8: Phylodynamics
Finlay Maguire
Module 8 Lecture Recording
Module 8 Lecture Slides
Lab
Day 5
Module 9: Mobile Genetic Elements
Rob Beiko
Module 9 Lecture Recording
Module 9 Lecture Slides
Lab
Module 9 Lab Instructions
Module 9 Lab Slides
Data file: MicroReactMatrix.tsv
Data file: Module9-core_gene_alignment.tre
Module 10: Emerging Pathogen Detection and Identification
Darian Hole
Module 10 Lecture Recording
Module 10 Lecture Slides
Lab
Module 10 Lab
Module 10 Lab Slides
Post-Workshop Materials
CourseData
Note that some of these files are quite large. If you have issues downloading them, try copying the link address, opening a new blank tab, and entering the URL into the new tab’s address bar. If that fails, contact us at support@bioinformatics.ca.
- integrated_assignment_1 data
- integrated_assignment_2 data
- module 5 data
- module 6 data
- module 7 data
- module 8 data
- module 9 data
- module 10 data
AMI
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_IDE_240509
- AMI ID: ami-09493b543784a1309
If you want to create and activate a new AWS account, please follow the instructions provided by Amazon.