Infectious Disease Genomic Epidemiology 2024
I Introduction
Workshop Info
Class Photo
Schedule
Pre-work
Meet Your Faculty
Data and Compute Setup
II Modules
Module 1: Introduction to Genomic Epidemiology
Lecture
Module 2: De Novo Genome Assembly and Annotation
Lecture
Lab
Integrative Assignment 1
Introduction
Required Tools
Core Genome SNV Analysis
Phylogenetic Analysis & Visualization
Genome Annotation
Integrative Assignment 2
Introduction
List of Software Utilized
Assignment Setup
Phylogenetic Construction
Nextclade Analysis
Recombination Analysis
Answer Key
Module 3: Data Curation and Data Sharing
Lecture
Lab
Data Curation and Sharing Lab
Excercise 1 Scenario
Lab Instructions
CanCOGeN Template Curation Reference Guide
EBI OLS Exercise
WHO Guiding Principles for Genomic Data Sharing
Module 4: Phylogenetic Analysis
Lecture
Module 5: Viral Pathogen Genomic Analysis - Single Nucleotide Variants
Lecture
Lab
Introduction
Data Sets
Data Download and Preparation
Running SIGNAL
Reference-based Assembly using SIGNAL
Quality Control and Assessment
Coverage Analysis
Module 6: Bacterial Pathogen Genomic Analysis - Genome-based Subtyping
Lecture
Lab
Introduction
Learning Objectives
Timeline for Training
Getting Started
Day 1: Pre-processing and Preliminary Analyses
Day 2: Visualizations to Facilitate Analysis
Module 7: Antimicrobila Resistant Gene (AMR) Analysis
Lecture
Lab
Module 8: Phylodynamics
Lecture
Lab
Module 9: Mobile Genetic Elements
Lecture
Lab
Data Files
Sponsors
Infectious Disease Genomic Epidemiology 2024
Module 9: Mobile Genetic Elements
Lecture
Lab
Data Files
MicroReactMatrix.tsv
Module9-core_gene_alignment.tre