From raw reads to an accessible pangenome: a path strewn with pitfalls and large stones

Francois Sabot

Francois Sabot, French National Research Institute for Sustainable Development, France


Current trends in various fields of biology aim to obtain pangenomes as a solution to represent the true diversity of species, integrating SNP and structural variations. However, eukaryotes, especially plants, face multiple problems such as assembly, genome comparison, and pangenome construction. During this talk, I will present the way we deal with these different limitations, from raw reads to pangenome vizualisation using rice species. I will mostly focus on the advantages of Oxford Nanopore long reads to obtain new high-quality genomes and non-reference sequences, as well as on our current development for integrating these new data into graph pangenomes.


After gaining a Ph.D. in Genetics, Francois Sabot worked on the evolution of transposable elements and genome structure. He is currently a senior scientist at the French National Institute for Sustainable Development (IRD). His topics are linked to pangenomics, such as pangenome graph creation, usage and vizualisation, impact of anthropization on the pangenome, and the relationship between species through pangenome comparison. Francois works mostly on rices, including Asian and African, but also insects (mosquitoes and Drosophilae), algae, and even some human pathogens.