Course Details

  • Date: October 19th, 2022 - November 9th, 2022
  • Time: 1:00 pm - 2:15 pm
  • Location: Online Webinar
  • Presenter(s): Alex Emmons (BTEP), Greg Caporaso (NAU), Samantha Chill (CCBR)
Welcome to the Microbiome Analysis with QIIME 2 course series!
This course series was designed to teach the basics of targeted amplicon data processing and analysis using the QIIME 2 platform. Attendees will learn how to format data and metadata, import data, denoise and classify sequences, and conduct basic analyses including measures of alpha and beta diversity.  Content from this course was inspired by and uses code from the QIIME 2 Cancer Microbiome Intervention Tutorial created by the QIIME2 developers. However, this course does not seek to duplicate tutorial materials available on the QIIME2 website but rather complement them.  We hope to provide a hands on learning environment where learners can test their skills and ask questions as we work through tutorial material and additional practice materials in optional help sessions.
This course series will include seven 1 – 1.25 hour lectures followed by a 45 minute optional practice session. Lessons will be on Mondays and Wednesdays from 1 – 2:15 pm. Help sessions will begin thereafter 2:15 – 3:00 pm.
(Note: Lesson 1 has a different meeting link.)
Lesson topics:
Lesson 2: Preparing the data, data import, and demultiplexing (Oct 24th)
Lesson 3: Trimming, read joining and quality filtering, OTU clustering / denoising (Oct 26th)
Lesson 4: Taxonomic classification, phylogeny, feature table filtering (Oct 31st)
Lesson 5: Alpha diversity (Nov 2nd )
Lesson 6: Beta diversity (Nov 7th)
Lesson 7: Course Wrap-up  (Nov 9th)
Course requirements:
Who can take this course?
There are no prerequisites to take this course. However, learners should have basic unix skills (e.g., know how to navigate directories, copy, move, and download files from the web). This course is open to NCI researchers interested in using the QIIME2 platform to process and analyze microbiome data.
What materials are needed to take this course?
To participate in this course, you will need a computer, a reliable internet connection, and a web browser. All classes and help sessions will be held virtually through Webex. This class will be taught using the GOLD learning environment on the DNAnexus platform. Learners will need to sign up for a DNAnexus account and send their user name to                 

Registering here will register you for all 7 lessons, including Lesson 1, which will provide an introduction to QIIME 2 by one of the leading developers of the QIIME 2 platform, Dr. Greg Caporaso. You do not need to register for each individual lesson. If you decide to register for this series after the start of the course, please send us an email at, and we will register you.