Infectious Disease Genomic Epidemiology
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: Phylogenetic Analysis
Lecture
AWS Setup
Module 3: Data Curation and Data Sharing
Lecture
Lab
Module 4: Viral Pathogen Genomic Analysis - Single Nucleotide Variants
Lecture
Lab
Virus Short-Read Genome Assembly and Variant Analysis
Module 5: Bacterial Pathogen Genomic Analysis
Lecture
Lab
Setup
Background
Learning Objectives
Analysis Dataset
Getting Started
cgMLST QC
Locus Quality
Defining Core Genes
Genome Quality
Hamming Distance
Dendrogram Construction
A Simple Tree Vis
Clustering by Distance
Cluster Analysis
Investigating Local Core Genes
Group Exercise
Module 6: Antimicrobial Resistant Gene (AMR) Analysis
Lecture
Lab
Introduction
CARD Website and Antibiotic Resistance Ontology
RGI for Genome Analysis
RGI at the Command Line
RGI for Merged Metagenomic Reads
Metagenomic Sequencing Reads and the KMA Algorithm
Pathogen of Origin Prediction
Module 7: Phylodynamics and Transmission Dynamics
Lecture
Lab
1. Introduction
2. List of Software for Tutorial
3. Exercise Setup
4. Phylodynamics Analysis
5. Visualizing the Phylodynamic Analysis Alongside Epidemiological Metadata
6. Selection Analysis
Module 8: Emerging Pathogen Detection and Identification
Lecture
1. Introduction
2. List fo Software for Tutorial and its Respective Documentation
3. Exercise Setup
4. Exercise
5. Final words
Keynote Lecture | Follow That Virus!: Genomics Leading the Way
Lecture
Module 9: Mobile Genetic Elements and Environmental Microbiome
Lecture
Lab
Sponsors
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Infectious Disease Genomic Epidemiology 2023
Module 1: Introduction to Genomic Epidemiology
Lecture