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

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.

The Trainers

  • Dr Mark Crowe

Workshop Dates

City Location Date Cost
Newcastle University of Newcastle 4th December 2015 $165.00 incl. GST

Draft Program

Time Topic
08:30 Introductions and workshop orientation
How to access Galaxy
NGS read mapping
10:00 Morning Tea
10:30 Visualising mapped data using genome browsers
Calling SNP and indel variants
Filtering for high quality calls
12:00 Lunch
13:00 Quality control and filtering of sequencing data
Introduction to advanced variant detection applications:MPiLeup, FreeBayes and GATK
15:00 Afternoon Tea
15:30 Comparison and evaluation of variant prediction list
Annotation of SNP effects
16:30 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 16th November 2015. Successful applicants will be notified no later than 20th November 2015.

The workshop fee of $165 (including GST) covers course material, computer access, lunch and refreshments.

If you are unable to apply online please download the application form and email the completed form to Andrew Gilbert.

Training Updates

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