ppanggolin

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robbedewin / PaRMMoSaHN

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

bioinformatics systems-biology computational-biology microbiology cobrapy sbml flux-balance-analysis pangenome genome-scale-metabolic-model metabolic-modeling ppanggolin gapseq

Updated May 26, 2026
Python

Qasim-Hussain-Code / ppanggolin_pangenomics_helicobacter_pylori

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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.

bioinformatics microbial-genomics comparative-genomics synteny phylogenomics pangenomics mafft resistome prokka fastani bacterial-genomics amrfinderplus iqtree2 helicobacter-pylori ppanggolin

Updated Aug 4, 2026
Python

Qasim-Hussain-Code / Nature2022_Spneumo_Pangenome

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

bioinformatics genomics phylogenomics pangenomics genomic-epidemiology streptococcus-pneumoniae ppanggolin amr-profiling

Updated Aug 4, 2026
Python

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