recipe sequana

A set of standalone application and snakemake pipelines dedicated to NGS (new generation sequencing) analysis



Developer docs:


BSD / BSD-3-Clause



package sequana

(downloads) docker_sequana



depends adjusttext:

depends bioservices:


depends brokenaxes:

depends bx-python:

depends click:


depends colorlog:


depends colormap:

depends cookiecutter:


depends cython:

depends deprecated:

depends docutils:

depends easydev:


depends gseapy:

depends itolapi:

depends lxml:

depends matplotlib-base:


depends matplotlib-venn:

depends mock:

depends multiqc:


depends packaging:

depends pandas:


depends plotly:

depends psutil:

depends pykwalify:

depends pysam:


depends python:


depends rich-click:

depends ruamel.yaml:


depends scikit-learn:

depends scipy:

depends seaborn:

depends selenium:

depends snakemake-minimal:


depends statsmodels:

depends tqdm:

depends upsetplot:

depends vcfpy:

depends xlrd:



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 sequana

and update with::

   mamba update sequana

To create a new environment, run:

mamba create --name myenvname sequana

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 `sequana/tags`_ for valid values for ``<tag>``)

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