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).

Haplotype matching capabilities on the GBWT

Utility for converting large GBZ files to a special format to read efficiently over the internet inside of a browser.

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

Analysis of shared parts of a pangenome

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.

Sequence-Level Pangenome Variation Graphs for Bacteriophages

Notes upon pangenome graphs construction

Library to parse, edit and handle in memory GFA graphs

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

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