tiramisutes / atlas

ATLAS - Three commands to start analysing your metagenome data

Metagenome-Atlas

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.

• check the samples.tsv
• edit the config.yaml
• run atlas on any cluster system For more details see documentation.

Assembly based metagenomics

Atlas is a easy to use metagenomic pipeline

Setup

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

License

BSD-3.

Citation

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data.
Kieser, S., Brown, J., Zdobnov, E. M., Trajkovski, M. & McCue, L. A.
BMC Bioinformatics 21, 257 (2020).
doi: 10.1186/s12859-020-03585-4