sbx_genomad is a sunbeam extension for identifying, assigning, and annotating viruses and plasmids in assemblies. This pipeline uses geNomad to achieve this with additional custom filtering steps that can be ignored if not needed.
Extension install is as simple as passing the extension's URL on GitHub to sunbeam extend
:
sunbeam extend https://github.com/Ulthran/sbx_genomad
Any user-modifiable parameters specified in config.yml
are automatically added on sunbeam init
. If you're installing an extension in a project where you already have a config file, run the following to add the options for your newly added extension to your config (the -i
flag means in-place config file modification; remove the -i
flag to see the new config in stdout):
sunbeam config update -i /path/to/project/sunbeam_config.yml
Installation instructions for older versions of Sunbeam are included at the end of this README.
To run an extension, simply run Sunbeam as usual with your extension's target rule specified:
sunbeam run --profile /path/to/project/ all_genomad
- genomad_db: Path to where genomad should install/pull its database from (directory not a filename)
- ref_fp: Path to the bacterial reference genome to map proviral contigs against
Installing an extension is as simple as cloning (or moving) your extension directory into the sunbeam/extensions/ folder, installing requirements through Conda, and adding the new options to your existing configuration file:
git clone https://github.com/sunbeam-labs/sbx_genomad/ sunbeam/extensions/sbx_genomad
cat sunbeam/extensions/sbx_genomad/config.yml >> sunbeam_config.yml
Please post any issues with this extension here.