ArticleBMC bioinformatics2025
PG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers.
Article in BMC bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
1 citing paper in PubMed.
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
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4 authors.
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Abstract
backgroundPangenome graphs integrate multiple assemblies to represent non-redundant genetic diversity. However, current evaluations of pangenome graphs rely primarily on technical parameters (e.g., total length, number of nodes/edges, growth curves), which fail to assess how effectively the graph represents homologous stretches across the integrated assemblies and how well short reads align against pangenome graph references.
resultsWe introduce a novel method to quantitatively assess how well a pangenome graph represents its integrated assemblies. Our method quantifies how many single-copy and universal k-mers from the source assemblies are uniquely and completely represented within the graph nodes. Implemented in the open-source tool PG-SCUnK, this approach identifies the fractions of unique, duplicated, and split k-mers, which correlate with short read mapping rates to the pangenome graph.
conclusionsInsights provided by PG-SCUnK facilitate the selection of appropriate parameters to build optimal reference pangenome graphs.
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