Abstract
Summary With the increasing availability of high-quality genome assemblies, pangenome graph is emerging as a new paradigm in genomics research for identifying, encoding, and interpreting the genetic variation landscape at the population and species levels. To facilitate a better examination of pangenome graph towards novel biological insights, here we present VRPG, a web-based interactive viewer of reference pangenome graph. Compared with its counterparts, VRPG is the only one to provide native and efficient support for rGFA-formatted reference pangenome graph, capable of visualizing large-scale reference pangenome graphs built upon hundreds of genome assemblies. Moreover, VRPG shines with its unique features in highlighting the path of any constitutive assembly along the graph as well as in presenting its corresponding presence/absence and copy number variation, which is highly valuable in both large-scale genome comparison and fine-scale structural variant analysis. To further demonstrate its features and scalability, we applied VRPG to the cutting-edge yeast and human reference pangenome graphs derived from hundreds of input assemblies via a dedicated website.
Availability and implementation VRPG is written in Python and HTML. It is free for use under the MIT license, available at https://github.com/codeatcg/VRPG.
Demonstration https://www.evomicslab.org/app/vrpg/
Contact yuejiaxing{at}gmail.com
Supplementary information Supplementary data are available at Bioinformatics online.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
better highlights the novelty and added value of VRPG compared with existing tools.