The use of a single reference genome in bioinformatics can lead to reference bias and miss important information about genome variability and relationships. New assembly methods have made it easier to generate high-quality complete genome assemblies and using a pangenome graph that expresses many genomes and their mutual alignment can help address these issues. This practical course will provide comprehensive training and collaboration opportunities in pangenomics, focusing on building and analyzing such graphs from whole genome assemblies.

The practical course is structured in modules over three days. Each day will begin with an introductory lecture followed by class discussion of key concepts in pangenomics. The remainder of each day will consist of practical hands-on sessions. These sessions will involve a combination of both mirroring exercises with the instructor to demonstrate specific skills as well as applying these skills independently to complete individual exercises. After and during each exercise, interpretation of results will be discussed as a group.

 The course will introduce biologists and bioinformaticians into the field of pangenome construction and analysis, as well as those involved in comparative genomics and the assembly of pangenomes for any species. It will include information useful for both beginners and more advanced users, with a focus on practical applications in pangenomic analysis and interpretation.
Attendees should have a background in biology and bioinformatics. The course will involve a mix of lectures and hands-on practical exercises using command line Linux, making a good knowledge of Linux operating system and basic shell commands a mandatory prerequisite. Participants should also be familiar with genomics data formats such as FASTA, VCF, and BED files, as these will be extensively used throughout the practical sessions.

 After completing this event, participants will be able to:

 - Build and analyze pangenome graphs from whole genome assemblies
 - Understand the relationships between multiple genomes
 -  Contribute to collaborative pangenome projects
 -  Implement pangenome-based analyses in their research

-  During the practical sessions, we will work with real pangenome datasets
-     Participants are welcome to bring their own data for discussion

-   Example datasets will be provided for all hands-on exercises

 Day 1 (3pm-8pm, Berlin time)

- Lectures: Introduction to pangenomics and pangenome graphs
      - What pangenome and pangenomics are
      - Pangenome graph building and visualization
      - Understanding pangenomes

- Practical: Building and understanding pangenome graphs
      - Setting up the computers/AWS (Amazon Web Services) instances
      - Building your first (small) pangenome graphs with PGGB (PanGenome Graph Builder)
      - Understanding pangenomes with ODGI (Optimized Dynamic Genome/Graph Implementation)

Day 2 (3pm-8pm, Berlin time)

- Lectures: Pangenome applications and partitioning
      - Heterologous recombination in the human pangenome
      - Reference-guided and reference-free pangenome partitioning

- Practical: pangenome partitioning, understanding, and graph building
      - Understanding pangenomes with other ODGI commands - primate pangenome
      - Sequence partitioning by chromosome - human pangenome
      - Sequence partitioning by community - yeast pangenome

Day 3 (3pm-8pm, Berlin time)

- Lectures: Implicit pangenomics and other pangenome applications
      - What implicit pangenomics is and why it matters
      - Lessons from the amylase locus
      - Pangenome-based genotyping

- Practical:
      - Implicit pangenome graphs with IMPG (IMplicit Pangenome Graph)
      - Graph-based haplotype deconvolution with COSIGT (COsine SImilarity GenoTyper)

Should you have any further questions, please send an email to info@physalia-courses.org