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 (we recommend running the above conda install command, to get all of the necessary dependencies):

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

Docker:

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