Research Object Crate for Metaenome-Atlas

# Metagenome-Atlas [](https://anaconda.org/bioconda/metagenome-atlas) [](https://anaconda.org/bioconda/metagenome-atlas) [](https://metagenome-atlas.readthedocs.io/en/latest/?badge=latest)  Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, to Annotation.  You can start using atlas with three commands: ``` mamba install -y -c bioconda -c conda-forge metagenome-atlas={latest_version} atlas init --db-dir databases path/to/fastq/files atlas run all ``` where `{latest_version}` should be replaced by [](https://anaconda.org/bioconda/metagenome-atlas) # Webpage [metagenome-atlas.github.io](https://metagenome-atlas.github.io/) # Documentation https://metagenome-atlas.readthedocs.io/ [Tutorial](https://github.com/metagenome-atlas/Tutorial) # 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](https://doi.org/10.1186/s12859-020-03585-4) # Developpment/Extensions Here are some ideas I work or want to work on when I have time. If you want to contribute or have some ideas let me know via a feature request issue. - Optimized MAG recovery (e.g. [Spacegraphcats](https://github.com/spacegraphcats/spacegraphcats)) - Integration of viruses/plasmid that live for now as [extensions](https://github.com/metagenome-atlas/virome_atlas) - Add statistics and visualisations as in [atlas_analyze](https://github.com/metagenome-atlas/atlas_analyze) - Implementation of most rules as snakemake wrapper - Cloud execution - Update to new Snakemake version and use cool reports.

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