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

Microbial Amplicon Analysis

This lesson aims to teach the fundamentals of microbial amplicon analysis. Although many genes can be amplified, in practice the most common are 16S rDNA (for bacteria) and ITS (Internal Transcribed Spacer) DNA for fungi, so that is what this lesson focuses on. We use public datasets to demonstrate the major components of the analysis pipeline, including dealing with sequencing data, turning sequence data into a table of counts, and running common analyses on that table, not to mention performing data cleaning at each step.

If you are interested in metagenomics (which uses random reads instead of specific amplicons), check out this other lesson under development.


This lesson uses command-line tools within the UNIX shell. Basic familiarity with the shell is expected but not required.


Setup Download files required for the lesson
00:00 1. Demultiplexing Reads How do I demultiplex reads?
00:00 2. Sequnece quality control How do I get my sequences ready to count?
00:00 3. Counting microbes with QIIME2-Deblur How do I tally microbes with QIIME2 and Deblur?
00:00 4. Counting microbes with DADA2 How do I tally microbes with DADA2?
00:00 5. Counting microbes with mothur How do I tally microbes with mothur?
00:00 6. Alpha Diversity What is alpha diversity and how do I calculate it?
00:00 7. Beta diversity What is beta diversity and how do I calculate it?
00:00 8. Finding Differentially Abundant Microbes How do I find whicih microbes are different in different samples?
00:00 Finish

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