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Article

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

GigaScience - 6 Jan 2025

Kopalli Venkataramana, Arslan Kübra, Morales-Díaz Noemia, Zanini Silvia F, Golicz Agnieszka A

Abstract excerpt

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...

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Identifiers

PMID: 41342577
DOI: 10.1093/gigascience/giaf121
PMCID: PMC12676463

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