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)

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

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

generating hardware accelerators for pangenomic graph queries

Long-read aligner to pangenome graphs

Optimal sequence-to-graph alignment with recombinations

AMR/VF LGT focused bacterial genomics analysis workflow

Construct and Analyze the North American Vitis pangenome

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

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

Pangenome Mutation-Annotated Networks

Pangenome Analysis in Prokaryotes Lesson

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.

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

Scripts for Hill et al. (in review) 🌾

Pangenome openness from k-mers

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