This lesson is still being designed and assembled (Pre-Alpha version)



All pre-requisites are taken care of if you are using this lesson at the Otago Bioinformatics Spring School 2021.

Please see the setup instructions if you wish to undertake this workshop on your own computer.


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).


Setup Download files required for the lesson
00:00 1. Metabarcoding Basics What are the main components of metabarcoding pipelines?
00:15 2. Demultiplexing and Trimming What are the different primer design methods for metabarcoding?
How do we demultiplex and quality control metabarcoding data?
00:45 3. Denoising or clustering the sequences Is it better to denoise or cluster sequence data?
01:30 4. Taxonomy Assignment What are the main strategies for assigning taxonomy to OTUs?
What is the difference between Sintax and Naive Bayes?
02:15 5. Creating A Reference Database What reference databases are available for metabarcoding
How do I make a custom database?
03:00 6. Statistics with R: Getting Started What R packages do I need to explore my results?
How do I import my results into R?
03:30 7. Statistics and Graphing with R How do I use ggplot and other programs with Phyloseq?
What statistical approaches do I use to explore my metabarcoding results?
04:30 8. Introduction to Qiime How do I import today’s results into Qiime?
04:45 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.