The Agent Skills Directory

Command Execution: The skill utilizes several Python and R scripts located within its internal plugin directory to automate bioinformatics tasks like data preflight, quality control, and ASV (Amplicon Sequence Variant) generation. These scripts, such as ngs_preflight.py and run_amplicon_microbiome.py, are used to wrap complex scientific tools into a streamlined workflow.
External Pipeline Integration: The instructions include patterns for running nf-core/ampliseq via Nextflow. nf-core is a widely recognized community initiative for reproducible bioinformatics pipelines, and its usage here is a standard method for performing marker-gene analysis using containers like Docker.

ngs-amplicon-microbiome