A Sunbeam extension for taxonomic assignment of reads to databases using Kraken. You can get pre-built kraken databases at the Kraken homepage or build your own then specify the path to your database in the config.
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_kraken.git
To generate a tsv-format report, create a project, specify your database, and use the all_classify target:
sunbeam init --data_fp /path/to/reads/ /path/to/project/
sunbeam config modify -i -f /path/to/project/sunbeam_config.yml -s 'sbx_kraken: {{kraken_db_fp: {/path/to/db}}}'
sunbeam run --profile /path/to/project/ all_classify
N.B. For sunbeam versions <4 the last command will be something like sunbeam run --configfile /path/to/project/sunbeam_config.yml all_classify.
- kraken_db_fp: Is the filepath to a kraken database
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_kraken.git extensions/sbx_kraken
and then include it in the config for any given project with:
cat extensions/sbx_kraken/config.yml >> /path/to/project/sunbeam_config.yml