Chapter 1 Introduction

Sequencing DNA barcodes from mixed sources of DNA is an increasingly used way to survey biodiversity, whether analysing dietary content from faecal-derived DNA or monitoring aquatic species from water-derived DNA. This course will give an overview of metabarcoding with different barcoding genes to target particular taxa. Using an example data set, we will go from raw sequence data through to assigning taxonomy to the sequence variants and some examples of downstream community analysis.

Sessions will start with a brief presentation followed by self-paced computer practicals guided by an online interactive book. The book will contain theory and practice code.

At the end of the course learners will be able to:

  • Utilise and understand the use of dada2 with metabarcoding data.
  • Import and quality assess sequences and generate ASVs with dada2.
  • Assign taxonomies to ASVs.
  • Produce alpha and beta diversity metrics & plots.

There are supplemental materials including normalisation, exporting data, classifying ASVs with GenBank and BLAST, and assigning taxa with MEGAN. These can be run through after the course by the learner.