recipe meta-sparse

SPARSE indexes reference genomes in public databases into hierarchical clusters and uses it to predict origins of metagenomic reads.



GPL3 / GNU General Public License v3 (GPLv3)



package meta-sparse

(downloads) docker_meta-sparse



depends bowtie2:

depends libgcc-ng:


depends mash:

depends msgpack-python:

depends numpy:

depends pandas:

depends pycapnp:

depends python:


depends python_abi:

2.7.* *_cp27mu

depends samtools:

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 meta-sparse

and update with::

   mamba update meta-sparse

To create a new environment, run:

mamba create --name myenvname meta-sparse

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 `meta-sparse/tags`_ for valid values for ``<tag>``)

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