On the optimization of copy number variations representation in pangenome graphs

Pangenome graphs often represent repeated stretches of DNA, such as Variable Number Tandem Repeats (VNTRs) and Copy Number Variations (CNVs), as separate alternative paths. This distorts the graph, makes alignment less reliable and the graph harder to read.

The paper introduces PANPHORTE, a method that detects these repeat-driven artifacts and rewrites them as explicit loops, without losing any information. On synthetic and real pangenome graphs, it increased exact read matches by up to 34.4% and reduced memory footprint by up to 71.7%, while making repeated regions much easier to spot visually.

Authors: Mirko Coggi, Lorenzo Basile, Beatrice Branchini, Gabriele Amodeo, Guido Walter Di Donato, Marco Domenico Santambrogio

Published in: Frontiers in Bioinformatics, 2026