recipe freyja

Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.



BSD / BSD-2-Clause



package freyja

(downloads) docker_freyja



depends biopython:

depends click:

depends cvxpy:

depends epiweeks:

depends ivar:

depends joblib:

depends matplotlib-base:

depends numpy:

depends pandas:

depends plotly:

depends pysam:

depends python:


depends pyyaml:

depends requests:

depends samtools:

depends seaborn:

depends tqdm:

depends usher:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install freyja

and update with::

   mamba update freyja

To create a new environment, run:

mamba create --name myenvname freyja

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `freyja/tags`_ for valid values for ``<tag>``)

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