recipe nanovar

Structural variant caller using low-depth long reads



GPL3 / GPL-3.0-or-later



package nanovar

(downloads) docker_nanovar



depends bedtools:


depends biopython:


depends libgcc-ng:


depends matplotlib-base:


depends minimap2:


depends natsort:


depends numpy:


depends progress:


depends pybedtools:


depends pysam:


depends python:


depends python_abi:

3.8.* *_cp38

depends samtools:


depends scipy:


depends tensorflow-mkl:




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 nanovar

and update with::

   mamba update nanovar

To create a new environment, run:

mamba create --name myenvname nanovar

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

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