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 com...
| Autores: | , , , , |
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| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2025 |
| País: | España |
| Institución: | Consejo Superior de Investigaciones Científicas (CSIC) |
| Repositorio: | DIGITAL.CSIC. Repositorio Institucional del CSIC |
| OAI Identifier: | oai:digital.csic.es:10261/413184 |
| Acceso en línea: | http://hdl.handle.net/10261/413184 https://api.elsevier.com/content/abstract/scopus_id/105023816520 |
| Access Level: | acceso abierto |
| Palabra clave: | Structural variation Benchmarking Crop genomics Pangenome graph |
| Sumario: | [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. |
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