Training Materials

This is a list of Pathogen Genomic Training resources. Courses we organise are available at https://uct-cbio.github.io/ngs-academy/courses/past-courses/

Title

Training Provider

Essential Background Theory for Genomic Epidemiology

CZ GEN EPI

Module	Title
Module 1	The overlapping timescales of pathogen evolution and transmission
Module 2	From sequencing to trees
Module 3	Shared terminology for describing phylogenetic trees
Module 4	Estimating evolutionary rates (molecular clocks) from sequence data
Module 5	Interpreting and working with evolutionary rates
Module 6	Using evolutionary rates to infer time trees

Online Applied Genomic Epi Handbook

CZ GEN EPI

Module	Title
Module 1	Applied genomic epidemiological handbook

Practicing Gaining Epidemiological Insights from Genomic Data

CZ GEN EPI

Module	Title
Module 1	Sequence alignments and molecular clocks
Module 2	Practice reading phylogenetic trees
Module 3	Applying the mutation report to disease surveillance work
Module 4	Epi Insights Part I: Assessing linkages between COVID-19 cases

Genetic Epidemiology

US CDC

Module	Title
Module 1	Introduction to epidemiology
Module 8	Analyzing and Interpreting Data

AMR Workshop 2021

PHA4GE

Module	Title	Presentation
Module 1	Introduction to databases and resources for AMR genomics	Presentation 1
Module 2	Theory and use of bioinformatics tools to detect AMR genes from genomes	Presentation 2
Module 3	Comparing and reporting AMR results using hAMRonization	Presentation 3
Module 4	AMR Genomics: Reads to Reports	Presentation 4

Rapid response resources

CZ BIOHUB

Module	Title
Module 1	Rapid response resources

Title

Training Provider