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Introduction to Eukaryotic Pangenomes#

Build, Analyze, and Manipulate a Pangenome Graph: from Construction to Genotyping#

Course Description#

Come and discover the exciting (and often obscure) world of pangenome graphs, and understand how this recent approach can help overcome the limits of traditional linear references.

This hands-on training will guide you step by step, from graph construction to variant calling, including visualization and extracting regions of interest. The training will be mostly practical, using real datasets from species such as rice or algae.

Objectives#

At the end of this course, participants will be able to:

  • Master the concepts of pangenomes and graphs, and understand the differences with a linear reference
  • Build a pangenome graph from several complete genomes using the PGGB and minigraph-cactus tools
  • Explore the graphs by computing global statistics (e.g., pangenome size, number of nodes, coverage) using the vg and gratools tools
  • Extract graph regions/loci based on positions or a list of individuals with the Gratools tool
  • Visualize graphs with the bandage or savanache software
  • Call variants and perform genotyping directly from the graph or from resequencing data aligned against a graph (giraffe, vg call)

This training will use real datasets, produced on models such as algae or rice.

Practical Information#

  • Duration: 2 days
  • Dates: September 29–30, 2025
  • Location: salle Badiane, Agropolis
  • City: Montpellier
  • Contact: bioinfo@ird.fr

Target Audience#

  • Open to the entire IRD community, with priority selection for people from the DIADE, PHIM, TRANSVIHMI, and MIVEGEC units (permanent staff, PhD students and postdocs, fixed-term contracts).

Prerequisites#

  • Own a laptop
  • Know basic Linux commands
  • Have an ongoing or planned project based on polymorphism detection (SNP, structural variations) and the use of several complete genomes

Course Coordinators#

Instructors UMR -- Role
François SABOT PANEEC Team / UMR DIADE logo_PANEEC logo_DIADE Lead instructor
Christine TRANCHANT PANEEC Team / UMR DIADE / i-Trop logo_PANEEC logo_DIADE logo_i-Trop Lead instructor