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 similarity
- allele/non-reference features-plots
- node plots resolved by length and coverage
- ...
Quickstart
- Install panacus using conda/mamba:
- Create a file
report.yamlwith the following content:
analyses:
- !Hist
count_type: Bp
- !Growth
coverage: 1,1,2
quorum: 0,0.9,0
- Run panacus:
- Take a look at the generated html file using your favorite browser!
For more info on what to write into report.yaml see the documentation.
Installation
From bioconda channel
Make sure you have conda/mamba installed!
From binary release
Linux x86_64
tar -xzvf panacus-0.4.1_x86_64-unknown-linux-musl.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="$(readlink -f panacus-0.4.1_x86_64-unknown-linux-musl/bin)":$PATH
# you are ready to go!
panacus --help
Mac OSX arm64
tar -xzvf panacus-0.4.1_aarch64-apple-darwin.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="$(readlink -f panacus-0.4.1_aarch64-apple-darwin/bin)":$PATH
# you are ready to go!
panacus --help
From repository
panacus requires a working RUST build system (version >= 1.74.1) to build from source. See here for more details.
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
Examples
Examples can be found in the examples directory. To get more information about how to use panacus check out the documentation.
Citation
Parmigiani, L., Garrison, E., Stoye, J., Marschall, T. & Doerr, D. Panacus: fast and exact pangenome growth and core size estimation. Bioinformatics, https://doi.org/10.1093/bioinformatics/btae720 (2024).