metagenome-atlas / atlas2anvio

Hand output of Atlas to Anvio

Snakemake workflow: Atlas2Anvio

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.

Authors

• Silas Kieser (@silask)

Usage

Step 1: Run Metagenome Atlas

See the docs for more details.

Step 2: Install the extension

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

Step 3: Execute workflow

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.

Step 4: launch the anvio interactive display

  snakemake -d atlas_working_dir interactive