We are pleased to announce the organization of the mini-symposium titled "Methods for Interfacing with Graphs of Genomic Sequences (MIGGS): Novel Pangenome Paradigms", which will be held on the afternoon of thursday (10/07) during JOBIM 2025 in Bordeaux.

With the recent advent of high-quality, telomere-to-telomere genome sequencing, pangenome approaches are now applicable to a broader range of genomes, including those of eukaryotes. Innovative models, such as pangenome graphs and huge k-mer databases, provide the ability to compare newly sequenced genomes against the full spectrum of known variations within a species or species complex. This approach mitigates analysis biases and has already demonstrated significant advantages, particularly in the study of complex structural variations.

The shift towards the paradigm of "pangenomes as the new reference" comes with novel challenges for our community, where analyses are traditionally reference-oriented rather than pangenome-based. However, tools and methodologies are rapidly diversifying, with related research and engineering efforts expanding across diverse fields, including microbiology, health, agronomy, and environmental sciences.

The objective of this mini-symposium is to bring together both new and experienced researchers engaged in, or simply curious about computational pangenomics, with some emphasis on graph-based models.

Here is a brief overview of the program:

– INVITED SPEAKER: JANA EBLER, Institute for Medical Biometry and Bioinformatics, Heinrich Heine University Düsseldorf, Germany

Title: Pangenome-based genome inference
Abstract: Typical analysis workflows map reads to a reference genome in order to genotype genetic variants. Generating such alignments introduces reference biases and comes with substantial computational burden. In contrast, recent k-mer based genotypers are fast, but struggle in repetitive or duplicated genomic regions. We introduced a new algorithm, PanGenie, that leverages a haplotype-resolved pangenome reference in conjunction with k-mer counts from short-read sequencing data to  genotype a wide spectrum of genetic variation – a process we refer to as  genome inference. Improvements are especially pronounced for structural variants (SVs) and variants in repetitive regions. We studied SVs across large cohorts sequenced with short-reads, using pangenome graphs generated by the HGSVC and HPRC  consortia, which enables the inclusion of these classes of variants in  genome-wide association studies.

– FLASH TALKS: 

Highlights of 8 JOBIM posters related to pangenomic approaches:

• Siegfried Dubois: "Pairwise edit distance between pangenome graphs"
• Lucien Piat: "Simulating structural variants in artificial populations using pangenomes"
• Martin Racoupeau: "Pan1c: A Snakemake Workflow for Chromosome-Level Pangenome Construction"
• Igor Martayan: "Fast estimation of pangenome openness using prefix-free parsing"
• Romane Junker: "Integrases as Key Players in Shaping Pangenome Hotspots in Enterobacteriaceae"
• Bastien Degardins: "Visualisation of diverse pangenomes using Vizitig"
• Camille Carette: "GraTools, easy manipulation of GFA1"
• Pauline Lasserre-Zuber: “Breed Wheat Pangenome Graphs” (not eligible for the prize)
• Antoine Malet: "GrAuFlow: A snakemake workflow for pangenome graph augmentation using short-read data"

[update 15/07/2025] Bastien Degardins was awarded the prize for best flash talk (a science outreach visual created by a professional scientific illustrator).

– ROUND TABLE: 

1. Do we need a pangenome graph?
2. What is a good pangenome?

A debate moderated by a panel of developers and users. Everyone is welcome, from experienced developers to researchers wondering if these approaches may be beneficial to their research.

Participation is open to all Jobim participants. Registration for the mini-symposium is made when registering for JOBIM (https://jobim2025.labri.fr/), which opens on May 15.

We hope to meet you there!

For the mini-symposium committee: Sèverine Bérard, Guillaume Gautreau, Claire Lemaitre, Benjamin Linard, Camille Marchet, Jean Monlong, François Sabot