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Unlock the Power of Pangenome Graphs


Learning Objectives

Participants in this course will gain an understanding of pangenome concepts and acquire hands-on experience in constructing and analyzing pangenome graphs. By the end of the course, they will have developed a comprehensive understanding of pangenome methods centered around whole genome assemblies. This will empower them to apply these methods to complex research questions that necessitate an understanding of the relationships between multiple genomes, or that require accounting for variability when analyzing new genomes.


Lesson Overview Time
1. Intro Introduction to pangenome graphs 30 min
Break 10 min
2. Setup Setup instructions for the tools and data used in this course 30 min
3. PGGB Introduction to the PGGB toolkit and its logic 30 min
Break 10 min
4. Running Running the command to construct a graph and discuss key parameters 45 min
Lunch 45 min
5. Evaluate Evaluating the constructed graph through MultiQC reports 60 min
Break 10 min
6. Variants Extracting variants from a graph 45 min


  • We extend our sincere appreciation to Assistant Professor Erik Garrison and his team at the University of Tennessee Health Science Center for their valuable guidance, suggestions, and feedback during the development of the pangenome graph pipeline.

Further reading and Extracurricular materials

After this course you might want to learn more about pangenome graphs and start using them in your own research, below are some great resources to help with that.

Documentation: - PGGB comes with rich documentation that explains key concepts and parameters:

Examples and lectures: - MemPan23 hosted a 3 day course and semniar series, check out there resources and lectures: