SaVanache: indexing and visualizing pangenome variation graphs

Abstract

With the rapid increase in genome sequencing and the growing availability of genomic resources, genomics is shifting toward pangenome representations that capture intra- and inter-specific diversity by integrating multiple genomes into a single entity. These pangenomes are increasingly modeled as graphs, encoding complex genomic variations in structures such as de Bruijn or variation graphs. However, while genome browsers provide standard and effective solutions for visualizing single or limited numbers of genomes, equivalent interactive tools for graph-based pangenomes remain limited, particularly for variation graph models. We developed SaVanache, a multi-resolution visualization interface designed to explore pangenome variation graphs at various depths. SaVanache enables the exploration of both global diversity and structural variations (SVs) across genomes relative to a user-defined linear pivot genome. Unlike synteny viewers, SaVanache emphasizes variations by representing SV types through a dedicated set of glyphs, facilitating intuitive one-to-many comparisons. To support smooth exploration, SaVanache preprocesses a Graphical Fragment Assembly (GFA) pangenome file into optimized index and data structures, enabling fast, real-time queries on large pangenome graphs. By combining advanced visualization techniques with e[ff]icient data handling, SaVanache provides a robust tool for scientists to analyze and visualize genetic variation within genomes and pangenomes. SaVanache is open source and freely available at https://forge.ird.fr/diade/savanache, with a public web instance at https://savanache.ird.fr.