recipe graftm

GraftM is a pipeline used for identifying and classifying marker gene reads from metagenomic datasets



GPL3 / GPL3+



package graftm

(downloads) docker_graftm



depends biom-format:


depends biopython:


depends bird_tool_utils_python:

depends dendropy:


depends diamond:


depends extern:

depends fastalite:

depends fasttree:

depends hmmer:


depends jinja2:

depends krona:


depends mafft:


depends mfqe:


depends orfm:


depends pplacer:

depends python:


depends pyyaml:

depends taxtastic:




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 graftm

and update with::

   mamba update graftm

To create a new environment, run:

mamba create --name myenvname graftm

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

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