PG-SCUnK: measuring pangenome graph representativeness using Single-Copy and Universal K-mers

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. 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 pangenome graphs. Availability and implementationA bash implementation of the PG-SCUnK workflow is freely available under the GNU GPLv3 license at https://github.com/cumtr/PG-SCUnK/.