recipe smallgenomeutilities

A collection of scripts that are useful for dealing with viral RNA NGS data.



GPL2 / GNU General Public License v2 or later (GPLv2+)



package smallgenomeutilities

(downloads) docker_smallgenomeutilities



depends bcbio-gff:

depends biopython:

depends mafft:

depends matplotlib-base:

depends numpy:

depends pandas:

depends progress:

depends pysam:


depends pysamstats:

depends python:


depends pyyaml:

depends scikit-learn:

depends scipy:



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 smallgenomeutilities

and update with::

   mamba update smallgenomeutilities

To create a new environment, run:

mamba create --name myenvname smallgenomeutilities

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

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