Plasmid Atlas

This workflow is designed to run mataplasmidspades on the output of metagenome atlas

Authors

• Silas Kieser (@silask)

Dependencies

conda or vibrant

Usage

This extension should be used after the running metagenome-atlas at least until the assembly step.

./plasmid_atlas atlas_working_directory path/to/store/databases {other snakemake arguments}

or directly call snakemake snakemake -d atlas_working_directory --config database_dir="path/to/store/databases"

For more detailed configuration see the config/template_config.yaml

Cluster execution

Execute the workflow locally via

snakemake --cores $N

using $N cores or run it in a cluster environment via

snakemake --cluster qsub --jobs 100

or

snakemake --drmaa --jobs 100

See the Snakemake documentation for further details.