recipe autometa

Automated extraction of genomes from shotgun metagenomes







An automated binning pipeline for metagenomes, in particular host-associated and highly complex ones. Miller, I. J.; Rees, E. R.; Ross, J.; Miller, I.; Baxa, J.; Lopera, J.; Kerby, R. L.; Rey, F. E.; Kwan, J. C. Autometa: Automated extraction of microbial genomes from individual shotgun metagenomes. Nucleic Acids Research, 2019. DOI:

package autometa

(downloads) docker_autometa



depends attrs:

depends bedtools:

depends biopython:

depends bowtie2:

depends diamond:


depends gdown:

depends hmmer:

depends numba:


depends numpy:


depends pandas:


depends parallel:

depends prodigal:


depends python:


depends requests:

depends rsync:

depends samtools:


depends scikit-bio:

depends scikit-learn:


depends scipy:

depends seqkit:

depends tqdm:

depends trimap:

depends tsne:

depends umap-learn:




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 autometa

and update with::

   mamba update autometa

To create a new environment, run:

mamba create --name myenvname autometa

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

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