https://github.com/neherlab/pangraph
A bioinformatic toolkit to align genome assemblies into pangenome graphs
https://github.com/neherlab/pangraph
bacteria bioinformatics genome genome-assembly julia pangenome pangraph
Last synced: 19 days ago
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A bioinformatic toolkit to align genome assemblies into pangenome graphs
- Host: GitHub
- URL: https://github.com/neherlab/pangraph
- Owner: neherlab
- License: mit
- Created: 2020-06-28T10:46:15.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2025-03-27T15:47:53.000Z (27 days ago)
- Last Synced: 2025-03-27T16:41:45.006Z (27 days ago)
- Topics: bacteria, bioinformatics, genome, genome-assembly, julia, pangenome, pangraph
- Language: C
- Homepage: https://docs.pangraph.org
- Size: 75.7 MB
- Stars: 101
- Watchers: 7
- Forks: 7
- Open Issues: 13
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
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README
# PanGraph
[](https://docs.pangraph.org/)
> a bioinformatic toolkit to align large sets of closely related genomes into a graph data structure
> [!WARNING]
> Pangraph is currently undergoing a major migration between v0 and v1. In this short transition period links and documentation may be inconsistent.
## Overview
**pangraph** provides a command line interface to find homology amongst large collections of closely related genomes.
The core of the algorithm partitions each genome into _blocks_ that represent a sequence interval related by vertical descent.
Each genome is then an ordered walk along _blocks_. The collection of all genomes form a graph that captures all observed structural diversity.
**pangraph** is a standalone tool useful to parsimoniously infer horizontal gene transfer events within a community; perform comparative studies of genome gain, loss, and rearrangement dynamics; or simply to compress many related genomes.
The original implementation of pangraph (version v0) was implemented in Julia and was described in the publication [Noll, Molari, Shaw and Neher, 2023](https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001034).
The current version (v1) is a reimplementation of the original algorithm in Rust by Ivan Aksamentov and Marco Molari.
The new implementation should be much easier to install and is faster in many use cases.
## Installation
Pangraph is available:
- as a **standalone binary**
- as a **docker container**
For more extended instructions on installation please refer to the [documentation](https://docs.pangraph.org/category/installation).
### Standalone binary
This is the recommended way to install Pangraph. You can download the latest release for your operating system [from here](https://docs.pangraph.org/installation/standalone).
### Docker container
PanGraph is available as a Docker container:
```bash
docker pull neherlab/pangraph:latest
```
See the [documentation](https://docs.pangraph.org/installation/with-docker) for extended instructions on its usage.
## Examples
Please refer to the [tutorials within the documentation](https://docs.pangraph.org/category/tutorial) for an in-depth usage guide.
For a quick reference, see below.
Align a multi-fasta `sequences.fa` in a graph:
```bash
pangraph build sequences.fa -o graph.json
```
Extract the core-genome alignment from the graph, with blocks appearing in the order of the reference genome `NC_010468`:
```bash
pangraph export core-genome graph.json \
--guide-strain NC_010468 \
-o core_genome_aln.fa
```
Export the graph in gfa format for visualization:
```bash
pangraph export gfa graph.json -o graph.gfa
```
Reconstruct input sequences from the graph:
```bash
pangraph reconstruct graph.json -o sequences.fa
```
## PyPangraph
PyPangraph is a python package with convenient utilities to load and explore the graph data structure, see the [documentation](https://docs.pangraph.org/pypangraph/about-pypangraph) for installation instructions and more examples.
```python
import pypangraph as pp
graph = pp.Pangraph.load_graph("graph.json")
print(graph)
# pangraph object with 15 paths, 137 blocks and 1042 nodes
```
## Citation
If you use PanGraph in scientific publications, please cite the original paper presenting the algorithm:
*PanGraph: scalable bacterial pan-genome graph construction*
Nicholas Noll, Marco Molari, Liam P. Shaw, Richard A. Neher
Microbial Genomics, **9**(6), 2023; doi: [10.1099/mgen.0.001034](https://doi.org/10.1099/mgen.0.001034)
## License
[MIT License](LICENSE)
> [!NOTE]
> The legacy v0 version of Pangraph is now stored on the [`v0` branch](https://github.com/neherlab/pangraph/tree/v0) of the repository, and legacy documentation is available [here](https://v0.docs.pangraph.org/).