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

strange cross-platform, performance-oriented and interactive pangenome and large graph visualization

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

Practical Haplotype Graph (PHG) version 2

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

Repository for the FantasticLamp pipeline

A Geometric Framework for Pangenome Graph Alignment via Ricci Flow

Statistics and analysis for GFA files

Pangenome-based zygosity matrices.

Print genome sequences as paths in a compacted de Bruijn graph (GFA).

Analysis of shared parts of a pangenome

ODGI: understanding pangenome graphs (https://doi.org/10.1093/bioinformatics/btac308)

Library to parse, edit and handle in memory GFA graphs

Uncovering IS-mediated discord in bacterial genomes

Scripts for de-novo genome assembly, assembly polishing, QC and post-assemble analyses of HiFi whole genome sequence data and downstream pangenomics analyses to identify structural variants

Leveraging WES short reads for PAN-EXOME creation and analysis.

This repository provides a comprehensive module on graphical pangenomics, guiding users through building, indexing, mapping, and visualizing pangenome graphs. The module runs on Google Cloud Platform using Jupyter notebooks and includes tools like PGGB, vg, BLAST, and Bandage.