Installation

Freyja is entirely written in Python 3, but requires preprocessing by tools like iVar and samtools mpileup to generate the required input data. We recommend using python3.7, but Freyja has been tested on python versions up to 3.10.

Install via Conda:

conda install -c bioconda freyja

Local build from source:

git clone https://github.com/andersen-lab/Freyja.git
cd Freyja
pip install -e .

Please note that pip will not install all the requirements. You need to install some requirements via Conda by following these steps:

conda create -n freyja
conda activate freyja
conda env update --file environment.yml

Docker:

docker pull staphb/freyja
docker run --rm -it staphb/freyja [command]