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

• Silas Kieser (@silask)

conda or vibrant

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 snakemakesnakemake -d atlas_working_directory --config database_dir="path/to/store/databases"

For more detailed configuration see theconfig/template_config.yaml

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 theSnakemake documentation for further details.