A Counting Tool for Pangenome Graphs

panacus is a tool for calculating statistics for GFA files. It supports GFA files with P and W lines, but requires that the graph is blunt, i.e., nodes do not overlap and consequently, each link (L) points from the end of one segment (S) to the start of another.

panacus supports the following calculations:

• coverage histogram
• pangenome growth statistics
• path-/group-resolved coverage table

Coverage Histogram

Histogram listing the number of features (nodes, edges, ...) that are visited by a certain number of paths.

Pangenome Growth statistics

Describes how many features (nodes, edges, ...) one would expect on average if the graph was built from 1...n haplotypes.

To limit the amount of features that are part of the calculation (e.g. for visualizing the core genome) pairs of the coverage/quorum parameters can be used:

• coverage: include only features in the calculation that are visited by at least that many paths (can be used e.g. to filter out private nodes, that are part of only 1 haplotype)
• quorum: fraction of haplotypes that must share a feature after the haplotype is added to the graph to include it in the output (e.g. a quorum of 1 means only features that are shared by 100% of the haplotypes ("core genome"))

Installation

panacus is written in RUST and requires a working RUST build system (version >= 1.74.1) for installation. See here for more details.

panacus provides a Python script for visualizing the calculated counting statistics. It requires Python>=3.6 and the following Python libraries:

• matplotlib
• numpy
• pandas
• scikit-learn
• scipy
• seaborn

From bioconda channel

Make sure you have conda/mamba installed!

mamba install -c conda-forge -c bioconda panacus

From binary release

Linux x86_64

wget --no-check-certificate -c https://github.com/marschall-lab/panacus/releases/download/0.2.3/panacus-0.2.3_linux_x86_64.tar.gz
tar -xzvf panacus-0.2.3_linux_x86_64.tar.gz

# install the Python libraries necessary for panacus-visualize
pip install --user matplotlib numpy pandas scikit-learn scipy seaborn

# suggestion: add tool to path in your ~/.bashrc
export PATH="$(readlink -f panacus-0.2.3_linux_x86_64/bin)":$PATH

# you are ready to go! 
panacus --help

Mac OSX arm64

wget --no-check-certificate -c https://github.com/marschall-lab/panacus/releases/download/0.2.3/panacus-0.2.3_macos_arm64.tar.gz
tar -xzvf panacus-0.2.3_macos_arm64.tar.gz

# install the Python libraries necessary for panacus-visualize
pip install --user matplotlib numpy pandas scikit-learn scipy seaborn

# suggestion: add tool to path in your ~/.bashrc
export PATH="$(readlink -f panacus-0.2.3_macos_arm64/bin)":$PATH

# you are ready to go! 
panacus --help

From repository

git clone [email protected]:marschall-lab/panacus.git

cd panacus
cargo build --release

mkdir bin
ln -s ../target/release/panacus bin/
ln -s ../scripts/panacus-visualize.py bin/panacus-visualize

# install the Python libraries necessary for panacus-visualize
pip install --user matplotlib numpy pandas scikit-learn scipy seaborn

# suggestion: add tool to path in your ~/.bashrc
export PATH="$(readlink -f bin)":$PATH

# you are ready to go! 
panacus --help

Run

$ panacus
Calculate count statistics for pangenomic data

Usage: panacus <COMMAND>

Commands:
  histgrowth          Run in default mode, i.e., run hist and growth successively and output the results of the latter
  hist                Calculate coverage histogram from GFA file
  growth              Construct growth table from coverage histogram
  ordered-histgrowth  Compute growth table for order specified in grouping file (or, if non specified, the order of paths in the GFA file)
  table               Compute coverage table for count type
  help                Print this message or the help of the given subcommand(s)

Options:
  -h, --help     Print help
  -V, --version  Print version

Quickstart

Generate a simple growth plot from a GFA file:

RUST_LOG=info panacus histgrowth -t6 -q 0.1,0.5,1 -S <INPUT_GFA> > output.tsv
panacus-visualize -e output.tsv > output.pdf

Examples

Examples can be found in the examples directory.

Citation

Parmigiani, L., Garrison, E., Stoye, J., Marschall, T. & Doerr, D. Panacus: fast and exact pangenome growth and core size estimation. 2024.06.11.598418 Preprint at https://doi.org/10.1101/2024.06.11.598418 (2024).