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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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PG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers.

Tristan Cumer¹, Sotiria Milia², Alexander S Leonard²

¹Animal Genomics, ETH Zurich, Zurich, Switzerland. t.cumer.sci@gmail.com.

BMC Bioinformatics

|December 31, 2025

Summary

We developed PG-SCUnK to evaluate pangenome graph quality by analyzing k-mer representation. This method helps optimize graph construction for better genetic diversity representation and short read mapping.

Keywords:

Graph quality assessment Graph representativeness Pangenome graphs Single-copy k-mers Universal k-mers

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Area of Science:

Genomics
Bioinformatics

Background:

Pangenome graphs integrate multiple assemblies for non-redundant genetic diversity representation.
Current evaluations use technical parameters, not assessing homologous stretch representation or read alignment effectiveness.

Purpose of the Study:

To introduce a novel quantitative method for assessing pangenome graph representation of integrated assemblies.
To evaluate how well homologous genetic regions are captured and how short reads map to pangenome graphs.

Main Methods:

Developed a method to quantify unique and complete representation of single-copy and universal k-mers within pangenome graph nodes.
Implemented the method in the open-source tool PG-SCUnK.
Analyzed fractions of unique, duplicated, and split k-mers.

Main Results:

The method quantifies k-mer representation within pangenome graphs.
Fractions of unique, duplicated, and split k-mers correlate with short read mapping rates.
PG-SCUnK provides insights into graph quality.

Conclusions:

PG-SCUnK facilitates selection of optimal parameters for building reference pangenome graphs.
The tool aids in improving pangenome graph construction for better genomic analysis.