Species-agnostic pipeline that builds a pangenome-reference metabolic model and rapidly derives consistent, gap-filled strain-specific genome-scale models from bacterial genomes.

Structural pangenomics pipeline for Streptococcus pneumoniae (n=36) using Prokka annotation, PPanGGOLiN graph partitioning, IQ-TREE phylogenomics, and AMRFinderPlus profiling.

Graph-based pangenomic and synteny analysis of Helicobacter pylori (n=41 complete RefSeq genomes) using PPanGGOLiN, with reproducible workflows for annotation (Prokka), ANI quality control (FastANI), core-genome phylogeny (MAFFT + IQ-TREE 2), resistome profiling (AMRFinderPlus), and publication-grade visualizations.