recipe symbiontscreener

Symbiont-Screener is a reference-free approach to identifying high-confidence host's long reads from symbionts and contaminants and overcoming the low sequencing accuracy according to a trio-based screening model.






package symbiontscreener

(downloads) docker_symbiontscreener



depends kmer-jellyfish:

depends libgcc-ng:


depends libstdcxx-ng:


depends libzlib:


depends meryl:

depends numpy:

depends pandas:

depends plotly:

depends seqkit:

depends zlib:



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 symbiontscreener

and update with::

   mamba update symbiontscreener

To create a new environment, run:

mamba create --name myenvname symbiontscreener

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

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