VRPG: an interactive visualization framework for reference-projected pangenome graph

With the increasing availability of high-quality genome assemblies, pangenome graph is emerging as a new paradigm in the genomics field for identifying, encoding, and interpreting genomic variation landscape at both population and species levels. However, it remains a major challenge in understanding and interpretating pangenome graph via biologically informative visualization. To facilitate a better examination of pangenome graph towards novel biological insights, here we present VRPG, a web-based interactive visualization framework of pangenome graph. VRPG provides dynamic and efficient supports for exploring and annotating pangenome graphs along a reference-based coordinate system. Moreover, VRPG shines with its unique features in highlighting the directed path of any graph-constitutive assembly as well as in denoting copy number variation of genomic segments represented by graph-constitutive nodes, which are highly valuable in genome comparison and variant analysis. Additionally, VRPG enables side-by-side visualization between pangenome graph and reference-based annotation features, bridging the graph and linear genome context. To further demonstrate its features and scalability, we applied VRPG to the cutting-edge yeast and human reference pangenome graphs derived from hundreds of high-quality genome assemblies via a dedicated website (https://www.evomicslab.org/app/vrpg/). Contact: yuejiaxing@gmail.com Key pointsDeveloped an intuitive visualization framework for pangenome graph. Empowered graph-based feature highlighting and variant visualization. Enabled connecting reference-based annotation features in the context of pangenome graph.