Microbiome amplicon analyses

• This tutorial outlines the basics concepts in Plasmodium amplicon (i.e. 16S) analyses

Learning outcomes

• Explain various terminology and concepts associated with microbiomes
• Recognise the three primary diversity measures
• Compare and critique various methodologies for microbiome profiling
• Execute data cleaning and diversity measure analyses using QIIME-2

Prerequisites

• It is recommended that you have Notepad++ (Windows) or BBEdit (Mac) for viewing fasta files; most linux default editors can do this.
• It is recommended that you have followed the Concepts in Computer Programming, UNIX tutorial (basics) and Setting up and using conda tutorials if you are going to do the QIIME-2 worksheet.

Approximate time to finish tutorial

• Lecture: 30 mins
• Tutorials: 1 hour

Presentation

During the presentation there are points to stop and do exercises, which are linked below. The answers to the questions in the exercises are linked within each one.

• Download slides here

Worksheets

Microbiome 16S amplicon sequencing processing with QIIME-2 (via UNIX)

Microbiome 16S amplicon sequencing processing with Mothur (via Galaxy)

Other tutorials/tools

• Mothur tutorial
  • An alternative to QIIME-2 for 16S amplicon sequenced microbiome analyses
• Various QIIME-2 tutolorials:
  • “Atacama soil microbiome” tutorial
  • John Quensen tutorial
  • Youtube video tutorial
• Open & Reproducible Microbiome Data Analysis Spring School 2018