mb-pipeline

Code for analyzing metabarcoding (FoodSeq) datasets in the David Lab at Duke University. For full documentation, see the FoodSeq Handbook.

Repository Structure

mb-pipeline/
├── pipeline/          # Cluster scripts and R notebook for creating phyloseq objects
├── reference/         # Reference databases and samplesheet templates
└── foodseq-protocols/ # Wet lab protocols

Getting Started

1. Clone this repository to your HPC cluster
2. Install the foodseq.tools R package
3. Follow the instructions in pipeline/ or the FoodSeq Handbook