A Sunbeam extension for identifying inversion sites in metagenomic reads using PhaseFinder.
To install, activate your conda environment (using the name of your environment) and use sunbeam extend:
conda activate <i>sunbeamX.X.X</i>
sunbeam extend https://github.com/sunbeam-labs/sbx_phase_finder.git
To generate an inversions.txt summary file, create a project, specify your reference, and use the all_phase_finder target:
sunbeam init --data_fp /path/to/reads/ /path/to/project/
sunbeam config modify -i -f /path/to/project/sunbeam_config.yml -s 'sbx_phase_finder: {{ref_fp: {/path/to/host/host.fa}}}'
sunbeam run --profile /path/to/project/ all_phase_finder
N.B. For sunbeam versions <4 the last command will be something like sunbeam run --configfile /path/to/project/sunbeam_config.yml all_phase_finder.
- ref_fp: Is the filepath to a reference genome
For sunbeam versions <3 or if sunbeam extend isn't working, you can use git directly to install an extension:
git clone https://github.com/sunbeam-labs/sbx_phase_finder.git extensions/sbx_phase_finder
and then include it in the config for any given project with:
cat extensions/sbx_phase_finder/config.yml >> /path/to/project/sunbeam_config.yml