PG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers.

ABSTRACT:

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 th

SUBMITTER: Cumer T 

PROVIDER: S-EPMC12859900 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature