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

ABSTRACT:

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 r

SUBMITTER: Kopalli V 

PROVIDER: S-EPMC12676463 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature