Introduction to Metagenomics


Bioplatforms Australia and CSIRO joint introduction to Metagenomics hands-on Bioinformatics Workshop 9-10th July 2014, ANU, Canberra.

What this course covers

Introduction to tools and workflows used to explore metagenomics sequence data.


  • Amplicon target population structure using QIIME
  • Whole metagenome shotgun processing using EMBL-EBI Metagenomics Portal
  • Whole metagenome shotgun processing using open access software
  • Quality control of metagenomic sequence data using FASTQC
  • Gene and functional prediction using InterProScan
  • Analysis and visualisation of results
  • Detecting/Identifying enriched gene processes and functions (GO)

Is this couse for me?

This course is aimed at bench biologists with little or no experience of bioinformatics who are working in the area of metagenomics. Some of the tools to be introduced on the course will require the use of Unix commands. We strongly recommend that you familiarise yourself with these. Free tutorials are available from: After this course you should be able to:

  • Evaluate and apply appropriate technologies and methodologies
  • QC of data sets
  • Apply basic workflows for amplicon based metagenomics
  • Apply basic workflows for whole genome shotgun metagenomics


Workshop Dates

City Location Date
Canberra ANU 9 – 10 July 2014

Draft Program

Day 1 – Amplicon-based metagenomics

Time Topic
9:00 Welcome and course expectations
9:15 Command line warm-up (Lecture/hands-on)
9:45 Introduction to NGS and overview of metagenomics (Lecture)
10:15 Work-flow exercises [15min]
10:30 Introduction to 16s (overview; platforms; pros/cons) (Lecture)
11:00 Tea Break
11:30 Quality control (Lecture)
12:00 Quality control (trimming, primers, FASTQC) (hands-on)
12:30 Taxonomic analysis of amplicon data (Lecture)
13:30 Lunch
13:45 Qiime tutorial: OTUs and taxonomy assignment (Hands-on)
15:15 Tea Break
15:45 Qiime tutorial: Alpha diversity and Beta diversity (Hands-on)
17:15 Informal Q&A session

Day 2 – Shotgun Metagenomics

Time Topic
9:00 Introduction to day 2
9:15 Introduction to WGS functional analysis
9:45 Metagenome assembly (Lecture/hands-on)
10:30 Tea Break
11:00 InterPro and GO for functional analysis
11:30 An introduction to the EBI Metagenomics portal (EMG) (Hands-on)
12:00 Lunch
13:00 Functional analysis using EMG (Hands-on)
13:30 Mining the EMG output using R – comparing assembled and unassembled data (Hands-on)
14:30 Tea Break
15:00 Data visualisation using emperor
15:30 Review of workflows and other methods / resources
16:00 Accessing the Australian Research Cloud
16:30 Data Submission (Lecture)
17:00 Informal Q&A, course evaluation

Registration and Payment

Registrations Closed.


For further information contact Andrew Gilbert ( or Annette Mcgrath (

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