Table of Contents

Online course (MSc/PhD level): Analysis of mosquito-derived 16S rRNA seq data using QIIME2; May 28, 2020 – July 9, 2020

Overview:

Driven by a passion for strengthening the capacity for mosquito genomics research in Africa, I have developed this 6-week course to help researchers interested in mosquito microbiome research analyze their data. While there is increasing interest in this research area, along with increasing access to molecular technologies, analysis of the resulting data remains a challenge, especially for scientists based in Africa. My hope with this is to help equip these scientists with the bioinformatics skills required to analyze their data, although anyone anywhere in the world can participate.

We will explore the QIIME 2™ platform for analysing mosquito microbiota (16S seq) data. We will go over basic concepts in microbial ecology/analysis of microbial ecology data, as well as walk through the QIIME2 ‘Moving Pictures’ tutorial together. There will be homework after each session, where you will apply what you have learned to your own data. We will review each week’s homework together in the subsequent session. Appended below is the course content. Please email me if you would like to participate or have any questions.

Goal: at the end of the course, you should be able to perform fundamental analysis of 16S rRNA seq data, and visualize outputs using QIIME2.

What you will need:

• A functioning computer with internet access and QIIME2 installed (we will use Version: 2020.2, please see installation guide)
• Basic linux skills (this may help)
• Note taking materials

Course content and timetable:

Sessions will occur on Thursdays, starting from May 28, 2020 to July 9, 2020; from 11.00-13.00 CET

Resources:

1. Qiime2 info: https://qiime2.org/
2. Qiime2 installation: https://docs.qiime2.org/2020.2/install/ we will use Version: 2020.2
3. Qiime2 moving pictures tutorial: https://docs.qiime2.org/2020.2/tutorials/moving-pictures/
4. Other Qiime2 tutorials: https://docs.qiime2.org/2020.2/tutorials/
5. Qiime2 forum: https://forum.qiime2.org/
6. Integrating Qiime2 and R: https://forum.qiime2.org/t/tutorial-integrating-qiime2-and-r-for-data-visualization-and-analysis-using-qiime2r/4121/23
7. Basic Linux commands for beginners: https://maker.pro/linux/tutorial/basic-linux-commands-for-beginners
8. What is metadata: https://www.opendatasoft.com/blog/2016/08/25/what-is-metadata-and-why-is-it-important-data
9. Example mosquito microbiome metadata template: https://github.com/nsadada/Mosquito-microbiome-perspective/blob/master/Metadata_template.csv
10. Description of metadata fields in the above template: https://github.com/nsadada/Mosquito-microbiome-perspective/blob/master/Table_1.csv