ArticleGigaScience2025
Toward a standardized framework for pangenome graph evaluation: assessing crop plant pangenome variation graph construction from multiple assemblies.
Article in GigaScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- Representation and detection of inversions in pangenome graphs.NAR genomics and bioinformatics · 2026Article
- Structural Variant benchmarking frameworks: Parameterization, matching logic, and evaluation assumptions presented through HG002 and NA12878.PLoS computational biology · 2026Article
- Structural Variation and Its Roles in Plant Genomes.Plants (Basel, Switzerland) · 2026Review
- PanGraphRNA: An efficient and flexible bioinformatics platform for graph pangenome-based RNA-seq data analysis.Journal of integrative plant biology · 2026Article
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- Accessing crop genetic diversity via pangenomics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- From plant pangenome assemblies to operational graph references.Frontiers in plant science · 2026Article
- Toward a standardized framework for pangenome graph evaluation: assessing crop plant pangenome variation graph construction from multiple assemblies.GigaScience · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
backgroundPangenomes 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.
resultsBy 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.
conclusionsThis 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.