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PG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers
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PG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers
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Journal Article
PG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers
2025
Overview
Background
Pangenome 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.
Results
We 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.
Conclusions
Insights provided by PG-SCUnK facilitate the selection of appropriate parameters to build optimal reference pangenome graphs.
Publisher
BioMed Central,Springer Nature B.V
