On the optimization of copy number variations representation in pangenome graphs.

Graph-based pangenome references often misrepresent Copy Number Variations (CNVs) and Variable Number Tandem Repeats (VNTRs) as alternative acyclic paths, which hinders downstream analyses, degrades alignment behavior, and reduces interpretability in graph visualizations. For these reasons, we introduce PANPHORTE, a topology-optimization methodology that detects repeat-driven misrepresentations within superbubbles and rewrites them into structures that more faithfully reflect the underlying biology. Given a pangenome graph annotated with haplotype paths, PANPHORTE identifies repetitive elements inside superbubbles, isolates shared repeat sequences across distinct subpaths, and refactors the graph by splitting nodes and introducing explicit cycles, encoding CNVs and VNTRs without loss of information. We provide a C++ command-line implementation of the proposed specifications, and a complementary pipeline that applies PANPHORTE followed by GFAffix to further reduce redundancy in regions not affected by repeat-induced artifacts. We evaluate PANPHORTE on synthetic and real pangenome graphs, showing reductions in memory footprint of up to 71.69%, improvements in exact read matches of up to 34.4%, and substantially clearer visual identification of repeated loci.