Do it yourself: Data analysis with DADA2

Here you will use the DADA2 software to analyse the provided data, using an ASV approach. This is a popular and well-established tool for this approach, although other pipelines/softwares are available that may run on different platforms or have particular advantages for certain studies or users (Hakimzadeh et al, 2023).

Have a go at using DADA2 yourself with this short practical set up in Google colab. You will start with Illumina MiSeq 12S data from lake water eDNA samples (Doble et al, 2019) from which the primers have been trimmed off using cutadapt.

Learning outcomes:

After completing the exercises in this practical you 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

   Do it yourself: DADA2 practical

Prerequisites for the DADA2 practical:

• The practical is hosted in a Google Colab notebook which requires an up-to-date web browser and an internet connection
• Experience with R is beneficial but not essential to follow along with the exercises

Please not that this Colab work is licensed under a Creative Commons Attribution 4.0 International (CC BY-NC-SA 4.0) license.