pangenome-graph

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.

Statistics and analysis for GFA files

Repository for the FantasticLamp pipeline

A Geometric Framework for Pangenome Graph Alignment via Ricci Flow

Pangenome-based zygosity matrices.

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

Analysis of shared parts of a pangenome

Sequence-Level Pangenome Variation Graphs for Bacteriophages

Notes upon pangenome graphs construction

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

Enhancing genomic prediction accuracy in cassava using a pangenome framework. This repository houses the pipeline for transitioning from linear reference genomes to pangenome graphs, capturing structural variations to predict complex yield and quality traits.

Library to parse, edit and handle in memory GFA graphs

🧬🍏✨ Graph-aware contextual annotation of targeted genomic features.

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.

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

OctoPan is a comprehensive, scalable WDL (Workflow Description Language) pipeline for whole-exome sequencing (WES) and whole-genome sequencing (WGS) analysis.