Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, to Annotation.

Scheme of workflow

Easy to use

You can start using atlas with three commands:

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

So easy a caveman could do it

Atlas has only one dependency: conda. All databases and other dependencies are installed on the fly. Atlas is based on snakemake which allows to run steps of the workflow in parallel on a cluster.

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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



Silas Kieser

Embedded Bioinformatician and PhD candidate