sbx_sga (Single Genome Assembly) is a sunbeam extension for isolate QC, assembly, and classification. This pipeline uses Mash for quality control, Shovill for bacterial isolate assembly, CheckM2 and QUAST for assembly QC, MLST for typing, Bakta for annotation, abriTAMR for AMR profiling, and Sylph for taxonomic classification.
Extension install is as simple as passing the extension's URL on GitHub to sunbeam extend:
sunbeam extend https://github.com/sunbeam-labs/sbx_sga
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/ example_rule
- mash_ref: the reference file for running Mash (should be a file ending in
.msh) - checkm_ref: the diamond database for running CheckM2 (should be a file ending in
.dmnd) - bakta_ref: the bakta reference database (should be a directory similar to
.../bakta_db/db/)
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_sga/ sunbeam/extensions/sbx_sga
cat sunbeam/extensions/sbx_sga/config.yml >> sunbeam_config.yml
Please post any issues with this extension here.