Variant Detection Using Galaxy

Variant Detection using Galaxy is a one-day, hands-on workshop that will cover the concepts of detecting small variants, including SNPs and small indels, from next-generation sequencing data. You will use and compare a number of popular detection tools, visualise variants using a genome browser, and annotate SNPs for predicting biological effects.

Course Outline

During this course you will learn about;

  • The tool and workflows of SNP and indel detection
  • Quality filtering and other techniques for improving SNP prediction accuracy
  • Comparison of variant detection software
  • the use of the Galaxy platform for variant detection analysis


Workshop Dates

City Location Date Cost
Sydney Children’s Medical Research Institute, Westmead 27th May 2016 $165.00 plus GST
If you are interested in the RNA-Seq Data Analysis Using Galaxy workshop at Children’s Medical Research Institute, Westmead, on the 26th May 2016, please visit the workshop webpage, here.

Recommended Participants

Variant Detection using Galaxy is designed for bench scientists, PhD students and early career postdoctoral researchers who are planning to work with next-generation sequencing data for small variant detection. No prior bioinformatics experience required. This workshop will priorities medical researchers in a NSW or ACT based organisation, however all Australian life scientist are invited to apply.

Please note that you will need to bring your own laptop to this workshop, with either Firefox or Chrome installed. Unfortunately, tablet-style devices are generally incompatible with these sessions.


Workshop Coordinator

Katherine Champ, Bioplatforms Australia (


Draft Program

Time Topic
09:00 Introductions and workshop orientation How to access Galaxy NGS read mapping
10:30 Morning Tea
11:00 Visualising mapped data using genome browsers Calling SNP and indel variants Filtering for high quality calls
12:30 Lunch
13:30 Quality control and filtering of sequencing data Introduction to advanced variant detection applications:MPiLeup, FreeBayes and GATK
15:30 Afternoon Tea
16:00 Comparison and evaluation of variant prediction list Annotation of SNP effects
15:00 Final wrap-up and close

Registration and Payment

Due to the practical component of this workshop, places are strictly limited to 25 participants. To manage the high demand, all workshop applicants are subject to a selection process and MUST complete the online application form to be considered for a place. Incomplete applications will not be considered. The application period closes 2nd May 2016. Successful applicants will be notified no later than 6th May 2016. The workshop fee of $165 (plus GST) covers course material, lunch and refreshments. If you are unable to apply online please download the application form and email the completed form to



For further information contact Katherine Champ,


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Interested in Hosting a Bioinformatics Workshop?

If you are interested in hosting a bioinformatics workshop at your local organisation or institute please contact Katherine Champ on