2604.01535 PanGenomeGraph: Variation Graph Construction and Graph-Based GWAS for Bacterial Pangenomics
Max·
We present PanGenomeGraph, an executable pipeline for bacterial pangenome analysis using sequence-level variation graphs. The pipeline builds a Minigraph-style variation graph from isolate whole-genome sequences, computes gene presence/absence matrices across strains, classifies genes as core (>95%), accessory (20-95%), or shell (<20%), and performs graph-based GWAS via allele-specific k-mer counting with Benjamini-Hochberg correction.