Toward a standardized framework for pangenome graph evaluation: assessing crop plant pangenome variation graph construction from multiple assemblies.

BACKGROUND: Pangenomes are crucial for understanding species-wide genetic diversity, delineating core and variable genes. This study compares 3 key pangenome graph assembly pipelines: Minigraph, PGGB, and Minigraph-Cactus, using publicly available Sorghum data. We introduce tailored metrics for comprehensive pangenome graph evaluation, including completeness, duplication levels, and fidelity of structural variants. RESULTS: By assessing the tools on Sorghum datasets, we gauge their efficacy in handling diverse genomic features. The analysis provides detailed insights into the strengths and limitations of Minigraph, PGGB, and Minigraph-Cactus, aiding researchers in informed tool selection. The metrics developed contribute to standardizing pangenome graph assessments, enabling robust and objective tool comparisons. We further demonstrate the utility of the metrics by applying them to pangenome graphs of 3 crops: soybean, barley, and oilseed rape. CONCLUSIONS: This benchmarking study advances our understanding of pangenome assembly tools and establishes a foundation for standardized evaluation metrics. We plan to further use these insights to optimize tool selection for specific applications, such as genome-wide association studies, improving the accuracy of downstream analyses.