This snakemake script is an extension to metagenome-atlas. It allows the genomes predicted by Atlas and the coverages of them to be visualized and post processed in Anvi'o.
- Silas Kieser (@silask)
See the docs for more details.
If you simply want to use this workflow, download and extract the latest release. If you intend to modify and further develop this workflow, fork this repository. Please consider providing any generally applicable modifications via a pull request.
In any case, if you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository and, if available, its DOI (see above).
You probably want to install anvio:
conda install anvio
Run the snakemake of the extension in the same working dir as Atlas:
snakemake -d atlas_working_dir --cores $N
See the Snakemake documentation for further details.
snakemake -d atlas_working_dir interactive