sbx_shotgun_unifrac is a sunbeam extension for assigning shotgun reads to a bacterial tree of life and performing population statistics like UniFrac. This pipeline uses bwa for initial alignment steps and QIIME2 with the GreenGenes plugin for the reference phylogeny and performing the core methods.
Extension install is as simple as passing the extension's URL on GitHub to sunbeam extend:
sunbeam extend https://github.com/sunbeam-labs/sbx_shotgun_unifrac
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_shotgun_unifrac
- threads: Number of threads to use with
bwa - green_genes_fp: Directory with all GreenGenes reference files
- green_genes_version: Version of the GreenGenes db (E.g. "2024.09")
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_shotgun_unifrac/ sunbeam/extensions/sbx_shotgun_unifrac
cat sunbeam/extensions/sbx_shotgun_unifrac/config.yml >> sunbeam_config.yml
Please post any issues with this extension here.