recipe anvio

A platform for integrated multi-omics


Developer docs:


GPL3 / GPL-3.0-or-later



package anvio

(downloads) docker_anvio



depends anvio-minimal:


depends bioconductor-qvalue:

depends blast:

depends bowtie2:

depends bwa:

depends centrifuge:

depends diamond:

depends fastani:

depends fasttree:

depends hmmer:

depends iqtree:

depends mcl:

depends megahit:

depends muscle:

depends prodigal:

depends r-base:

depends r-magrittr:

depends r-optparse:

depends r-stringi:

depends r-tidyverse:

depends samtools:

depends spades:

depends trimal:

depends trnascan-se:



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 anvio

and update with::

   mamba update anvio

To create a new environment, run:

mamba create --name myenvname anvio

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

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