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ATLAS - Three commands to start analysing your metagenome data
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Version Bioconda CircleCI Documentation Status follow on twitter Slack

Quick Start

Three commands to start analysing your metagenome data:

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

All databases and dependencies are installed on the fly in the directory databases.

You want to run these three commands on the example data. If you have more time, then we recommend you configure atlas according to your needs.

Assembly based metagenomics

Atlas is a easy to use metagenomic pipeline

scheme of workflow


Atlas should be run on a linux sytem, with enough memory (min ~50GB but assembly usually requires 250GB). The only dependency is the conda package manager, which can easy be installed with anaconda. We recommend you to create a conda environment for atlas to avoid any conflicts of versions.

    conda create -y -n atlasenv
    source activate atlasenv
    conda install -y -c bioconda -c conda-forge metagenome-atlas

And you can run atlas. All other dependencies are installed in specific environments during the run of the pipeline.

For local execution we have also a docker container




We have a BioRxiv preprint please cite:

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data Silas Kieser, Joseph Brown, Evgeny M Zdobnov, Mirko Trajkovski, Lee Ann McCue bioRxiv 737528; doi:


This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, nor any jurisdiction or organization that has cooperated in the development of these materials, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents that its use would not infringe privately owned rights.

Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or Battelle Memorial Institute. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.


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