e-learning
Identifying tuberculosis transmission links: from SNPs to transmission clusters
Abstract
In a disease outbreak situation, to understand the dynamics and the size of the outbreak, it is essential to detect transmission clusters to distinguish likely outbreak cases from unrelated background cases. Such detection is nowadays often based on actual sequencing data that enables quantitative conclusions about differences between pathogen isolates.
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Learning Objectives
- Create a SNP alignment
- Calculate pairwise SNP distances between MTB samples
- Identify transmission clusters based on SNP distances
- Study the emergence and spread of drug resistance based on transmission analysis.
Licence: Creative Commons Attribution 4.0 International
Keywords: Evolution, microgalaxy, one-health, prokaryote
Target audience: Students
Resource type: e-learning
Version: 12
Status: Active
Prerequisites:
- Introduction to Galaxy Analyses
- M. tuberculosis Variant Analysis
- Using dataset collections
Learning objectives:
- Create a SNP alignment
- Calculate pairwise SNP distances between MTB samples
- Identify transmission clusters based on SNP distances
- Study the emergence and spread of drug resistance based on transmission analysis.
Date modified: 2024-07-12
Date published: 2022-03-16
Contributors: Wolfgang Maier
Scientific topics: Evolutionary biology, Genomics, Microbiology, Infectious disease, DNA polymorphism
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