Construction and analysis of eukaryotic pangenome graphs (30/11/2026 - 02/12/2026)
This training session is organized by the Genotoul-Bioinfo platform. This 2 days long course is dedicated to the construction and the analysis of eukaryotic pangenome graphs.
We will first present the concept of graph-based pangenome, then build one. We will then apply several tools for its analysis: use annotation, call variants, extract sub-graphs, visualize the graph, map reads, genotype individuals, and perform a GWAS on the graph. The different formats will also be presented.
By the end of the course, trainees will be familiar with the topic, and able to run the major tools made to build an exploit a pangenome graph.
This training is focused on practice. It consists of several modules with a large variety of exercises:
- First Day
- Start at 2 PM
- Presentation of the audience
- Introduction to pangenomics.
- Preparation and quality control of the genomes.
- Construction of a pangenome graph with Minigraph-Cactus
- End at 5 PM
- Second Day
- Start at 9 AM
- Presentation of the pangenome formats and indices.
- Transfer of annotation with GrAnnoT.
- Extraction of a sub-graph with vg
- Visualization with Bandage, SequenceTubeMap, PanAbyss.
- Calling variants with vg deconstruct, PanTree.
- Mapping reads with vg giraffe, presentation of mapping formats.
- End at 5 PM
- Third Day
- Start at 9 AM
- Surjecting mapped reads to a reference.
- Calling genotypes with vg call, pangenies
- GWAS with STOAT
- End at 12 PM maximum
The session will take place in the room ‘salle de formation’ at INRAE center of Toulouse-Auzeville, building C8.
Training materials are available at :
– slides and exercises: will be available here