sbx_metaphlan4

Introduction

sbx_metaphlan4 is a sunbeam extension for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) at the species-level. The pipeline uses MetaPhlAn4.

Installation

Extension install is as simple as passing the extension's URL on GitHub to sunbeam extend:

sunbeam extend https://github.com/sunbeam-labs/sbx_metaphlan4

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.

Running

To run an extension, simply run Sunbeam as usual with your extension's target rule specified:

sunbeam run --profile /path/to/project/ example_rule

Options for config.yml

• threads: Number of threads to use
• dbdir: Path to the directory the MetaPhlAn database is in (i.e. /path/to/db/)
• dbname: Name of the MetaPhlAn database (i.e. mpa_db)
• profile_strain: Profile strain to use with extract_markers.py and strainphlan
• reference_genome: A reference genome

Installing an extension (legacy instructions for sunbeam <3.0)

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_metaphlan4 sunbeam/extensions/sbx_metaphlan4
cat sunbeam/extensions/sbx_metaphlan4/config.yml >> sunbeam_config.yml

Issues with pipeline

Please post any issues with this extension here.