Course Overview

This course was designed to teach the basics of targeted amplicon data processing and analysis using the QIIME2 platform. Attendees will learn how to format data and metadata, import data, demultiplex sequences, trim sequences, denoise and classify sequences, and conduct basic analyses including measures of alpha and betadiversity.

Content from this course was inspired by the QIIME 2 Cancer Microbiome Intervention Tutorial provided by the QIIME2 developers. While much of the code used from that tutorial will be integrated into these lessons, this course does not seek to replicate tutorial materials already available on the QIIME2 website (See the QIIME2 youtube playlist for detailed lessons).

This course 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.

Lesson topics:

Lesson 1: Toward fully reproducible microbiome multi-omics bioinformatics with QIIME 2 (Oct 19th)

Lesson 1 will not include a hands on component, but rather will include an introduction to QIIME2 by guest speaker, Greg Caporaso, a leading developer of the QIIME2 platform.

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=c44af836ce9dd1631b58ccc285880a56

Lesson 2: Preparing the data, data import, and demultiplexing (Oct 24th)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=d7fca7b1d6b3441c445770782762c712

Lesson 3: Trimming, read joining and quality filtering, OTU clustering / denoising (Oct 26th)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=354bc1bfb92d6288a0c00ed0a7a1c777

Lesson 4: Taxonomic classification, phylogeny, feature table filtering (Oct 31st)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=b6ca607256a4e8c461487b40362fc51c

Lesson 5: Alpha diversity (Nov 2nd - CANCELLED). Lesson taught in combination with Lesson 6.

Lesson 6: Beta diversity (Nov 7th)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=b667466d9ae5f273cf273b6ecc7f93d1

Lesson 7: Course Wrap-up (Additional analyses to consider, feature table export, qiime2R import) (Nov 9th)

Recording link: https://cbiit.webex.com/cbiit/ldr.php?RCID=4d90e55b0adaebe54bff0ed5030783f3 .

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 ncibtep@nih.gov.