An analysis and visualization platform for 'omics data

Panacus is a tool for computing statistics for GFA-formatted pangenome graphs

Federating genomes with love (and synteny derived from functional annotations)

Optimal sequence-to-graph alignment with recombinations

generating hardware accelerators for pangenomic graph queries

GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.

Pangenome Mutation-Annotated Networks

Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions

An accurate aligner of long reads to a variation graph, based on co-linear chaining

Long-read aligner to pangenome graphs

Construct and Analyze the North American Vitis pangenome

AMR/VF LGT focused bacterial genomics analysis workflow

Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México

A pipeline for construction and graphical visualization of annotated pangenome networks.

Fast and Optimal Affine-Gap Sequence-to-Graph Alignment

Enumerating bubbles in pangenome graphs

Pangenome Analysis in Prokaryotes Lesson

Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.

Scripts and utilities for pangenomic/phylogenomic analysis of prokaryotic genomes. Scripts for the analysis of genomic features such as C-ARSC, N-ARSC, and intergenic spacer lengths are also included.

/ˈskuzi/

A nextflow pipeline to run the mummer pipelines (align genomes, call snps) and process outputs into sane formats.

A Geometric Framework for Pangenome Graph Alignment via Ricci Flow

Scripts for Hill et al. (2025) doi:10.1186/s12864-025-11432-0 🌾

Extension to the Crop Haplotypes website showing shared haplotypes between wheat genome assemblies. Enables mapping genomic regions of interest to the assemblies and calculate quality parameters such as alignment density or continuity

Topological data analysis for Comparative Genomics

Functions for working with NCBI's Pathogen Detection data

Pangenomic Statistical analysis in R (pasaR)

Plant Plastid-Mitochondria Pangenome-Graph Analysis Tool

A Snakemake workflow for microbial pangenomics analyses.

Repository dedicated to the experiment section of the paper: Revisiting pangenome openness with k-mers. PCJ Math & Comp Biol. (2024).