recipe metagenome-atlas

ATLAS - Three commands to start analysing your metagenome data



Developer docs


BSD / BSD-3-Clause



Atlas is a easy to use metagenomic pipeline ![scheme of workflow](

# Quick Start

Three commands to start analysing your metagenome data: ```

conda install -c bioconda -c conda-forge metagenome-atlas atlas init –db-dir databases path/to/fastq/files atlas run

``` All databases and dependencies are installed on the fly in the directory `db-dir`. You want to run these three commands on the example_data on the GitHub repo. If you have more time, then we recommend you configure atlas according to your needs.

- check the `samples.tsv` - edit the `config.yaml` - run atlas on any cluster system

For more details see documentation.

package metagenome-atlas

(downloads) docker_metagenome-atlas


2.1.3-0, 2.1.1-0, 2.0.6-1, 2.0.5-1, 2.0.4-1, 2.0.3-1, 2.0.1-1, 2.0.1-0

Depends bbmap


Depends biopython


Depends click


Depends git

Depends pandas


Depends python


Depends ruamel.yaml


Depends snakemake




With an activated Bioconda channel (see 2. Set up channels), install with:

conda install metagenome-atlas

and update with:

conda update metagenome-atlas

or use the docker container:

docker pull<tag>

(see metagenome-atlas/tags for valid values for <tag>)