Course Description: Evolutionary Epidemiology – Using Phylogenetics to Understand DR Emergence and Mtb Transmission
The Evolutionary Epidemiology course provides participants with a hands-on approach to using phylogenetics for understanding drug resistance (DR) emergence and Mycobacterium tuberculosis (Mtb) transmission using Illumina sequencing data. Through interactive Galaxy tutorials, participants will explore cluster analysis and phylogenetic methods to infer genetic relationships and transmission patterns.
This course is designed for researchers and students interested in evolutionary epidemiology, equipping them with essential computational skills for analyzing Mtb transmission dynamics and resistance evolution using short-read sequencing data.
What You’ll Learn
- Fundamentals of Phylogenetics: Understanding key phylogenetic principles in the context of Illumina sequencing.
- Interpreting Phylogenetic Trees: Inferring genetic distances and evolutionary relationships.
- Cluster Analysis: Identifying Mtb transmission clusters.
- SNP Thresholds and Transmission Events: Understanding genetic distances in relation to recent transmission.
- Drug Resistance Mutations: Recognizing de novo and transmitted resistance-conferring mutations.
- Hands-On Training: Running phylogenetic inference programs and calculating genetic distances using Illumina sequencing data.
By the end of this course, participants will be able to analyze and interpret phylogenetic data from Illumina sequencing, aiding in epidemiological investigations of Mtb transmission and drug resistance.
For more details, visit: Illumina Analysis Materials.
Lessons:
