This repository is designed to support assessment of plant dietary intake directly from human stool samples using DNA metabarcoding with the trnL-P6(UAA) marker1. It includes
- An experimental protocol to amplify trnL from DNA extracted from human fecal samples (details in trnL-pipeline/protocol)
- A computational pipeline to analyze high-throughput trnL amplicon sequencing data (in trnL-pipeline/pipeline)
- A reference database of trnL sequences for food plants used by humans to assign trnL reads to a plant taxon (in trnL-pipeline/reference)
These methods were developed by the David Lab at Duke University and accompany the manuscript "Diversity of plant DNA in stool is linked to dietary quality, age, and household income"2.