ggCaller traverses Bifrost graphs constructed from bacterial genomes to identify putative gene sequences, known as open reading frames (ORFs).
ggCaller incorporates Balrog to filter ORFs to improve specificity of calls and Panaroo for pangenome analysis and quality control.
Guides for installation, usage and a tutorial can be found here.
ggCaller is available on Linux. If you are running Windows 10/11, Linux can be installed via the Windows Subsystem for Linux (WSL).
We plan to get a MacOS version up and running in the future.
Install through bioconda:
conda install ggcaller
If conda is not installed, first install miniconda, then add the correct channels:
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
First, install Docker for your OS. If running with WSL2, you should still download Docker Desktop for Windows.
Then pull the latest image::
docker pull samhorsfield96/ggcaller:latest
To run ggCaller, run::
cd test && docker run --rm -it -v $(pwd):/workdir -v $(pwd):/data samhorsfield96/ggcaller:latest ggcaller --balrog-db /app/ggc_db --refs /workdir/pneumo_CL_group2_docker.txt --out /workdir/ggc_out
Required packages and versions can be found in environment_linux.yml
and environment_macOS.yml
depending on your operating system. In addition, a C++17 compiler (e.g. gcc >=7.3) is required.
For example, using conda (creates ggc_env
environment)
conda env create -f environment_linux.yml
conda activate ggc_env
Once all required packages are installed, install ggCaller using:
git clone --recursive https://github.com/samhorsfield96/ggCaller
cd ggCaller
python setup.py install
Please cite the ggCaller pre-print:
Horsfield, S.T., Croucher, N.J., Lees, J.A. "Accurate and fast graph-based pangenome annotation and clustering with ggCaller" bioRxiv 2023.01.24.524926 (2023). doi: https://doi.org/10.1101/2023.01.24.524926
If you use this code, please also cite the dependencies:
Succinct Data Structure Library 3.0 <https://github.com/xxsds/sdsl-lite>
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