I Introduction
Workshop Info
Class Photo
Schedule
AWS Setup Instructions
Meet Your Faculty
Data and Compute Setup
Module 1 Data Curation and Data Sharing
Lecture
Lab
Background
Exploring data heterogeneity across repositories
DataHarmonizer demonstration
Curation using the DataHarmonizer
Using EBI OLS to identify controlled vocabulary
Module 2 Emerging Pathogen Detection and Identification
Lecture
Lab
1. Introduction
2. List of software for tutorial and its respective documentation
3. Exercise setup
4. Exercise
Assembly-free approach
Assembly-based approach
5. Final words
Module 3 Pathogen Typing
Lecture
Lab
Introduction
PART ONE: chewBBACA Objective
PART TWO: cgMLST clustering Objective
Module 4 Outbreak Analysis
Lecture
Lab
Background
Set-Up
Cluster Identification
SNP Analysis
Transmission Inference
Module 5 Phylodynamics
Lecture
Lab
Table of contents
1. Introduction
2. List of software for tutorial
3. Exercise setup
4. Maximum likelihood phylodynamic analysis
5. Visualizing the phylodynamic analysis
6. Delphy analysis
7. End of lab
Keynote Presentation
Slides
Sponsors
Pathogen Genomic Epidemiology 2025
Keynote Presentation
Slides