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Metagenome-Atlas

Version Bioconda Documentation Status follow on twitter

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

You can start using atlas with three commands:

    mamba install -y -c bioconda -c conda-forge metagenome-atlas=2.9
    atlas init --db-dir databases path/to/fastq/files
    atlas run all

Webpage

metagenome-atlas.github.io

Documentation

https://metagenome-atlas.readthedocs.io/

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

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)
  • Integration of viruses/plasmid that live for now as extensions
  • Add statistics and visualisations as in atlas_analyze
  • Implementation of most rules as snakemake wrapper
  • Cloud execution
  • Update to new Snakemake version and use cool reports.