Instructors name and contact information

  • Shuangbin Xu:
    • Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
  • Supervisor: Guangchuang Yu

Workshop description

This workshop focuses on the bioinformatics analysis of microbiome. Specifically, we will demonstrate how to perform downstream analysis (after OTU picking) using MicrobiotaProcess and phyloseq.


  • Basic knowledge of R syntax.
  • General understanding of Amplicon analysis or have strong interests.
  • Familiarity with some bioconductor objects or S4 class.
  • A computer that runs on Unix-like system.

How to run Docker

R / Bioconductor packages used

Time outline

Activity Time
overview of Amplicon-Seq 3m
pipeline of Amplicon-Seq analysis 4m
Downstream analysis 10m
+ rarefraction curve
+ Alpha and beta analysis
+ Biomarker discovery
+ etc.
Hands-on demonstration 20m
Q/A section 5m

Workshop goals and objectives

Learning goals

  • Understand the basic idea of microbiome.
  • Identify the commonly practiced tools used in downstream analysis of microbiome.
  • Understand the common analysis of microbiome.

Learning objectives

  • Get familiar with the package MicrobiotaProcess and phyloseq.
  • Perform different analysis of microbiome.
  • Get familiar with the visualization of microbiome.