Welcome to Metabarcoding at Cefas!

Here at Cefas, Metabarcoding is central to many genomics projects. This tutorial space is designed to help anyone at Cefas start to carry out Metabarcoding work.

As a starting point, check out the Metabarcoding section.

Note

This project is under active development. PLease get in touch if you note any important omissions or errors. Please email nicola.coyle@cefas.co.uk with suggestions or queries.

Contents

• Metabarcoding
  • What is metabarcoding?
  • General Process:
  • Quality Control: Read quality
  • Clustering
  • Identifying Chimeras
  • Taxonomic assignment:
  • Diversity Statistics
• Resources
  • Visually explore data and statistics
  • Pipelines
  • Statistical analysis
  • Exploring functional implications of community structures:
  • Taxonomy
  • Papers, chapters and commentary:
• Dada2
  • Dada2 - Background & Installation
  • DADA2 Usage
  • Dada2 Tutorial
  • Alternative tutorial:
  • Dadaist2
  • Plotting Taxonomy Dadaist2 vs PhyloSeq
  • Follow up Statistics:
• Frogs
  • Frogs - Background & Installation
  • Tutorial
  • Parameter Considerations
• Statistics
  • Normalisation
  • To rarefy or to not rarefy
  • Alpha Diversity
  • Beta Diversity
  • Differential Abundance
• Azure Virtual Machine for Metabarcoding
  • GUI - graphical user interface
  • Command-line
• Glossary
• API

— Author: Nicola Coyle 25/01/2022