- recipe autometa
Automated extraction of genomes from shotgun metagenomes
- Homepage:
- Documentation:
- License:
AGPL / AGPL-3.0
- Recipe:
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: https://doi.org/10.1093/nar/gkz148
- package autometa¶
- versions:
2.2.3-0
,2.2.2-0
,2.2.1-0
,2.2.0-0
,2.1.0-0
,2.0.3-0
,2.0.2-0
,2.0.1-0
,2.0.0-0
- depends attrs:
- depends bedtools:
- depends biopython:
>=1.82
- depends bowtie2:
- depends diamond:
>=2.0
- depends gdown:
- depends hmmer:
- depends numba:
>=0.47
- depends numpy:
>=1.13
- depends pandas:
>=1.5
- depends parallel:
- depends prodigal:
>=2.5
- depends python:
>=3.7
- depends requests:
- depends rsync:
- depends samtools:
>=1.11
- depends scikit-bio:
- depends scikit-learn:
>=1.3
- depends scipy:
- depends seqkit:
- depends tqdm:
- depends trimap:
- depends tsne:
- depends umap-learn:
>=0.5
- requirements:
Installation
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 quay.io/biocontainers/autometa:<tag> (see `autometa/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
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