a bioinformatic toolkit to align large sets of closely related genomes into a graph data structure
pangraph provides both a command line interface, as well as a Julia library, to find homology amongst large collections of closely related genomes. The core of the algorithm partitions each genome into pancontigs that represent a sequence interval related by vertical descent. Each genome is then an ordered walk along pancontigs; 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 core algorithm and command line tools are self-contained and require no additional dependencies. The library is written in and thus requires Julia to be installed on your machine.
pangraph is available:
- as a julia library
- as a Docker container
- it can be compiled into a relocatable binary
For more extended instructions on installation please refer to the documentation.
To install pangraph as a julia library in a local environment:
# clone the repository git clone https://github.com/neherlab/pangraph.git && cd pangraph # build the package julia --project=. -e 'using Pkg; Pkg.build()'
The library can be accessed directly by entering the REPL:
Alternatively, command-line functionalities can be accessed by running the main
# example: build a graph from E.coli genomes julia --project=. src/PanGraph.jl build -c example_datasets/ecoli.fa.gz > graph.json
Note that to access the complete set of functionalities, the optional dependencies must be installed and available in your
PanGraph is available as a Docker container:
docker pull neherlab/pangraph:latest
See the documentation for extended instuctions on its usage.
pangraph can be built locally on your machine by running (inside the cloned repo)
export jc="path/to/julia/executable" make pangraph && make install
This will build the executable and place a symlink into
jc is not explicitly set, it will default to
vendor/julia-$VERSION/bin/julia. If this file does not exist, we will download automatically for the user, provided the host system is Linux or MacOSX.
Moreover, for the compilation to work, it is necessary to have MAFFT and mmseqs2 available in your
$PATH, see optional dependencies.
Note, it is recommended by the PackageCompiler.jl documentation to utilize the officially distributed binaries for Julia, not those distributed by your Linux distribution. As such, compilation may not work if you attempt to do so.
pangraph can optionally use mash, MAFFT, mmseqs2 or fasttree for some optional functionalities, as explained in the documentation.
For use of these functionalities, it is recommended to install these tools and have them available on
Alternatively, a script
bin/setup-pangraph is provided to install both tools into
bin/ for Linux-based operating systems.
Please refer to the tutorials within the documentation for an in-depth usage guide. For a quick reference, see below.
Align a multi-fasta
sequence.fa and realign each pancontig with MAFFT
pangraph build sequence.fa | pangraph polish > graph.json
Export a graph
export/pangraph.gfa as GFA for visualization
pangraph export graph.json
Compute all pairwise graphs and estimate parsimonious number of events between strains.
Output all computed data to directory
pangraph marginalize graph.json -o pairs
PanGraph: scalable bacterial pan-genome graph construction Nicholas Noll, Marco Molari, Liam P. Shaw, Richard Neher bioRxiv 2022.02.24.481757; doi: https://doi.org/10.1101/2022.02.24.481757