eDNA Workshop, June 2021


eDNA Workshop, June2021


Advances in genomics over the past decade have greatly expanded the breadth of community ecology, and enabled fine scale study of many ecosystems. Environmental DNA (eDNA) is DNA material isolated from environmental substrates, including water, soil, air, or even within larger organisms (using a broader definition of ‘environment’). The eDNA samples can be amplified with PCR and sequenced with next-generation sequencing technologies to study the biodiversity of the environment, in a method called metabarcoding. In this workshop we will review the most common methods for metabarcoding in order to identify the taxonomic components and determine the relationship across these communities. Through a combination of demonstration and hands-on practicals, you will learn the basic concepts and core tools needed to analyse eDNA metabarcoding data for a wide range of studies.

The material for this course was developed by Hugh Cross and Gert-Jan Jeunen. Valuable contributions and suggestions were made by Ngoni Faya, Lucie Jiraska, Dinindu Senanayake, and Annabel Whibley, all of whom also helped teach the material.

This workshop is sponsored by Genomics Aotearoa and the New Zealand eScience Infrastructure (NeSI).

UPDATE: 12/07/2021

Jupyter notebooks

I have converted all Jupyter notebooks to webpages, and they are available from the following links:

1. Metabarcoding Basics

2. Demultiplexing and trimming

3. Denoising and clustering

4. Introduction to QIIME

5. Taxonomy assignment

6. Importing metabarcoding data into R

7. Getting started exploring data (template)

8. Graphing data with R

Creating custom databases

We did not have time to cover the topic of creating a custom database. We are working on a Python program to make this process easier. It is in the testing phase, but should be ready soon. We will post a link here when it is at least in Beta mode. In the meantime, there is a plug-in for Qiime that covers much of the same process, and it is already installed along with the Qiime module on NeSI. Here is a link to a tutorial that covers the main process

When and where?


University of Otago, Auckland Campus

385 Queen Street, #3&4

Auckland, 1141

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Preliminary Schedule


Time Topic
9:00 Welcome
9:15 Introduction to NeSI?
10:00 Introduction to BASH, pt 1
10:30 Morning Break
11:00 Introduction to BASH, pt 2
11:30 Introduction to R
12:30 Lunch
13:30 Overview of Metabarcoding
14:00 Initial Data Trimming and QC
14:45 Afternoon Break
15:15 OTU Clustering
16:30 End Day 1


Time Topic
9:00 Review Day 1
9:30 Introduction to Qiime
10:30 Morning Break
11:00 Taxonomy Assignment
12:00 Getting started exploring the data
12:30 Lunch
13:30 Introduction to diversity analyses
14:00 Alpha and Beta diversity
14:45 Afternoon Break
15:15 Diversity (continued)
15:45 Creating custom reference database (if time)
16:15 Wrap up: work on own
16:30 End Workshop