recipe autometa

Automated extraction of genomes from shotgun metagenomes

Homepage:

https://github.com/KwanLab/Autometa

Documentation:

https://autometa.readthedocs.io/en/latest/

License:

AGPL / AGPL-3.0

Recipe:

/autometa/meta.yaml

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:

2.2.0-0,  2.1.0-0,  2.0.3-0,  2.0.2-0,  2.0.1-0,  2.0.0-0

Depends:

• attrs

• bedtools

• biopython

• bowtie2

• diamond >=2.0

• gdown

• hdbscan

• hmmer

• joblib 1.1.0

• numba >=0.47

• numpy >=1.13

• pandas >=1.1

• parallel

• prodigal >=2.5

• python >=3.7

• requests

• rsync

• samtools >=1.11

• scikit-bio

• scikit-learn 0.24

• scipy 1.8.1

• seqkit

• tqdm

• trimap

• tsne

• umap-learn >=0.5

Required By:

• automappa

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install autometa

and update with:

conda update autometa

or use the docker container:

docker pull quay.io/biocontainers/autometa:<tag>

(see autometa/tags for valid values for <tag>)

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