A CLI tool for generating pathogen-specific barcodes for Freyja.
BarcodeForge requires Python >= 3.10 (tested on 3.10–3.13).
BarcodeForge is available on Bioconda:
conda install bioconda::barcodeforge
Install the latest version directly from the GitHub repository:
pip install git+https://github.com/gp201/BarcodeForge.git
Or clone the repository and install it locally:
git clone https://github.com/gp201/BarcodeForge.git
cd BarcodeForge
pip install .
For development (includes test and formatting tools):
pip install -e ".[dev-requirements,test-requirements]"
The following tools are required and must be installed separately via Conda
(from the bioconda and conda-forge channels):
conda install -c conda-forge -c bioconda usher ucsc-fatovcf
Once installed, run the tool with:
barcodeforge --help
For example, to generate a barcode:
barcodeforge barcode reference.fasta aligned.fasta tree.nwk lineages.tsv --threads 4 --prefix RSVa