recipe metagem

Generate context specific genome-scale metabolic models and predict metabolic interactions directly from metagenomic data







doi: 10.1093/nar/gkab815, biotools: metagem

package metagem

(downloads) docker_metagem



depends bedtools:


depends bwa:


depends concoct:


depends diamond:


depends fastp:


depends gtdbtk:


depends maxbin2:


depends megahit:


depends metabat2:


depends python:


depends r-base:


depends r-gridextra:


depends r-tidytext:

depends r-tidyverse:

depends samtools:


depends snakemake:




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 metagem

and update with::

   mamba update metagem

To create a new environment, run:

mamba create --name myenvname metagem

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

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