sbx_seeker is a sunbeam extension for discriminating between virus and phage sequences. This pipeline uses MEGAHIT for assembly of contigs and seeker for virus/phage discrimination.
N.B. If using Megahit for assembly, this extension requires also having sbx_assembly installed.
sunbeam extend https://github.com/Ulthran/sbx_seeker.git
Run with sunbeam on the target all_seeker,
sunbeam run --profile /path/to/project/ all_seeker
There are currently no config options for this extension.
git clone https://github.com/Ulthran/sbx_seeker.git extensions/sbx_seeker
cd extensions/sbx_seeker
cat config.yml >> /path/to/sunbeam_config.yml
Please post any issues with this extension here.