Mosquito-derived 16S rRNA seq data analysis using QIIME2

Photo by Dlanor S on Unsplash.

Table of Contents

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


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

Week 1; May 28, 2020Steps for analysing 16S rRNA seq data; Overview of QIIME2 & Moving pictures tutorial; 10 min break; Installation of QIIME2; Loading data into QIIME 2Install QIIME2 and load your data into QIIME2
Week 2; June 4, 2020Homework review/troubleshooting; Overview of reads quality control, denoising and visualization of reads statsComplete QC and denoising on your data; and visualize and explore your reads stats pre and post QC
Week 3; June 11, 2020CANCELLED; Nsa’s sickCheck out this tutorial in the meantime
Week 4; June 18, 2020Homework review/troubleshooting: How to identify factors that may be influencing data composition: 10 min break; Hands-on guided class exercise (linear regression)If applicable, perform linear regression on your data
Week 5; June 25, 2020Homework review/troubleshooting; Overview of taxonomic annotation and visualizations; 10 min break; Hands-on guided class exercise; Visualization tips and tricks if there is timeComplete taxonomic annotation on your data; and create visualizations of your outputs
Week 6; July 2, 2020Homework review/troubleshooting; Overview of alpha and beta diversity; 10 min break; Hands-on guided class exerciseComplete alpha and beta diversity analysis on your data; and create alpha and beta diversity visualizations of your outputs
Week 7; July 9, 2020Homework review/troubleshooting; Overview of differential abundance testing; 10 min break; Hands-on guided exercise; Classwork on your data; Review/troubleshootingI would highly encourage exploring other QIIME 2 tutorials and integrating QIIME2 and R


  1. Qiime2 info:
  2. Qiime2 installation: we will use Version: 2020.2
  3. Qiime2 moving pictures tutorial:
  4. Other Qiime2 tutorials:
  5. Qiime2 forum:
  6. Integrating Qiime2 and R:
  7. Basic Linux commands for beginners:
  8. What is metadata:
  9. Example mosquito microbiome metadata template:
  10. Description of metadata fields in the above template:
Nsa Dada, PhD
Nsa Dada, PhD
Founder and Lead
Mosquito Microbiome Consortium

Entomologist and microbial ecologist fascinated with microbial interactions that underpin insect evolutionary responses to changes in their habitats.