https://otagoedna.github.io/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).
I have converted all Jupyter notebooks to webpages, and they are available from the following links:
2. Demultiplexing and trimming
6. Importing metabarcoding data into R
7. Getting started exploring data (template)
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
Thursday, 24th June, 9:00 - 4:30
Friday, 25th June, 9:00 - 4:30
Location:
University of Otago, Auckland Campus
385 Queen Street, #3&4
Auckland, 1141
| 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 |