Seeing is believing: making sense of complex pangenome graphs

What is it about?

With the increasing availability of high-quality genome assemblies, pangenome graphs emerged as a new paradigm in the genomic field for identifying, encoding, and presenting genomic variation at both the population and species level. However, it remains challenging to truly dissect and interpret pangenome graphs via biologically informative visualization. To facilitate better exploration and understanding of pangenome graphs toward novel biological insights, here we present a web-based interactive visualization and interpretation framework for linear reference–projected pangenome graphs (VRPG). VRPG provides efficient and intuitive support for exploring and annotating pangenome graphs along a linear-genome-based coordinate system (e.g., that of a primary linear reference genome). Moreover, VRPG offers many unique features such as in-graph path highlighting for graph-constituent input assemblies, copy number characterization for graph-embedding nodes, and graph-based mapping for query sequences, all of which are highly valuable for researchers working with pangenome graphs. Additionally, VRPG enables side-by-side visualization between the graph-based pangenome representation and the conventional primary linear reference genome–based feature annotations, therefore seamlessly bridging the graph and linear genomic contexts. To further demonstrate its functionality 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 web portal and examined their local genome diversity in the graph contexts.

Featured Image

Photo by MARIOLA GROBELSKA on Unsplash

Photo by MARIOLA GROBELSKA on Unsplash

Why is it important?

In this study, we developed VRPG, a web-based interactive framework for pangenome graph visualization and interpretation with full scalability, capable of rendering complex pangenome graphs derived from hundreds of genome assemblies. In addition to intuitive graphical visualization, VRPG also provides native supports for integrating conventional linear-genome-based feature annotations, enabling seamless examination of genomic variation in both graph-based and linear-based contexts. As further demonstrated with real world examples of yeast and human pangenome graphs as well as with benchmarking comparison with other tools, VRPG shines with its unique advantages in both functionality and scalability, making it a highly compelling choice for interactive and informative pangenome graph visualization.

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