Interactive visualization and interpretation of pangenome graphs by linear reference-based coordinate projection and...

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Pangenome graphs are a powerful new way to represent genomic variation across populations and species.
• Interpreting and visualizing these complex graphs for biological insights remains a significant challenge.

Purpose of the Study:

• To present VRPG, a web-based interactive framework for visualizing and interpreting linear reference-projected pangenome graphs.
• To facilitate exploration and annotation of pangenome graphs within a familiar linear genome coordinate system.

Main Methods:

• Developed VRPG, a web-based interactive visualization and interpretation framework.
• Implemented features for in-graph path highlighting, copy number characterization, and graph-based mapping.
• Enabled side-by-side visualization of pangenome graphs and linear genome annotations.

Main Results:

• VRPG provides efficient and intuitive exploration of pangenome graphs.
• Unique features facilitate detailed analysis of genomic variation, including copy number.
• Seamlessly bridges graph and linear genomic contexts for enhanced understanding.

Conclusions:

• VRPG effectively addresses the challenge of visualizing and interpreting pangenome graphs.
• The framework enhances biological insight discovery from complex genomic variation data.
• Demonstrated scalability and functionality using yeast and human pangenome graphs.