NGS Bioinformatics Workshop

Bioinformatics Workshop for Ecological and Evolutionary Research. 17-19th February, 2014. Deakin University, Waterfront Campus, Geelong.

The Centre for Integrative ecology (Deakin University) and Bio21 (Melbourne University) are pleased to be hosting a bioinformatics workshop from the 17th – 19th February 2014 at the Deakin University Geelong Waterfront campus.  This workshop is an intensive 3-day workshop and will combine seminars and invited talks with hands-on computation training by international experts. It will focus on the analysis of Genotype By Sequencing (GBS) a new method for generating large numbers of single nucleotide polymorphisms (SNPs) for use in genetic analyses.

NEW – A PDF copy of workshop slides are now available through the links below







Hands On Overview





Overview of workshop

A key aim of this workshop is to bring together researchers (higher degree research students, postdoctoral research fellows and academics) from around Australia that are using (or are planning to use) next generation sequencing approaches to address  questions in the fields of ecology and evolutionary biology.

The first day (17th February) will include introductory presentations giving an overview of the use of NGS data for ecological and evolutionary research. This will include seminars from invited speakers and short (5 minute) presentations by attendees to give an overview of their projects and how they are using (or are planning to use) NGS in their research. Places are limited to 70 people for day 1 (17th February) and there are no costs associated with attending the first day.

Days 2 and 3 will be dedicated to a series of lectures with emphasis on data analysis with current pipelines, illustrated with hands-on computer exercises. This will be run by experts from the University of Cornell’s Institute for Genomic Research, who developed the GBS approach. For more information on GBS please click here. Places for the workshop are limited to 40 people for day 2 & 3.

Registration and costs for bioinformatics workshop

Day 1: While there are no fees for attending the first day of the workshop, places are limited to 70 registration is essential.

Day 2 & 3: Seating is limited to 40 places for the second and third day of the workshop and will involve hands-on training and data processing of NGS data.  In order to ensure that applicants from a wide range of research groups can attend, an expression of interest needs to be submitted before applicants are accepted for registration. The deadline for expression of interest is 6th January 2014. Applicants will then be asked to formally register and pay by 20 January 2014.

The cost of the hand-on component of the workshop (day 2 and 3 only) is $100 and includes lunches, morning tea/coffee and a workshop dinner (18th February).

Pre-requisites: Delegates should be familiar with LINUX/UNIX environments and basic command lines.


Workshop documentation

TASSEL GBS pipeline command line documentation

Basic shell commands


Location:  Waterfront campus, Deakin University, 1 Gheringhap Street, Geelong, Victoria 3220


Invited speakers

Professor Luciano Beheregaray
School of Biological Sciences
Flinders University, Adelaide

Presentation title- “Ecological Genomics of Australian Rainbowfishes”

Background: Primary research focus on understanding biogeographic scenarios and evolutionary processes underlying population divergence and speciation in fishes.Past and current research includes work on fishes from Amazonia, Patagonia, Pampas, and southern Africa, coastal dolphins, sperm whales and blue whales from the Indian and Pacific Oceans, giant tortoises from the Galapagos, sharks, rays and sea turtles from Mexico and central America, lizards from the Brazilian Cerrado; and wombats, sharks, bony fishes, molluscs, crustaceans, tunicates and sea-urchins from Australia.

Dr Gordana Rasic
Pest and Disease Vector Group
Bio21 Institute, Department of Genetics
The University of Melbourne

Presentation title- “Ecological genomics of the yellow fever mosquito – implications for the Wolbachia-based strategies to suppress dengue fever”

Background: Information from single nucleotide polymorphisms (SNPs) can now facilitate the transfer of genome data into the more effective measures for controlling disease vector populations. In the case of the main vector of dengue, Aedes aegypti, we use a novel control strategy that employs the release of individuals infected with the bacterium Wolbachia pipientis. Insights into mosquito dispersal, ovipositing behaviour, as well as the potential changes in its genome after the Wolbachia introduction, are crucial for the successful strategy implementation. To be able to track these processes, a large number of SNP markers are needed. We use a cost-effective double digest Restriction Associated DNA sequencing (RADseq) to explore genome-wide variation in a high throughput manner.

Associate Professor Justin Borevitz
Research School of Biology
College of Medicine, Biology and Environment
Australian National University, Canberra

Presentation title-  “Genomics for Adaptation: Phenome to Biome, Model Organism tools for Foundation Species”

Background: Research focuses on Genome Wide Association Studies in Arabidopsis and next generation genotyping by sequencing in emerging model organisms. Current work includes the identifing the genetic basis of local adaptation to seasonal climates using Phenomic and Landscape Genomic approaches in plant model organisms and foundation species.

Accommodation and airport transfers:

Service Adult fare Concession fare More details
Gull Bus Tullamarine airport to Geelong train station $30.00 single$55.00 return $18.00 single$34.00 return
Airport Shuttle Avalon airport to Geelong train station From $17.00 From $17.00
V/line rail Southern cross station  (Melbourne CBD) to Geelong station $7.80 single$15.60 return $3.90 single$7.80 return

Accommodation prices may vary depending on time of booking.

Irish Murphy’s Hostel,
30 Aberdeen Street, Geelong, (03) 52214335 or online
$40 – $45 per night

Nireeda Apartments on Clare,
1-3 Clare St, Geelong, (03) 5221 0566
From $99 per night

Comfort Inn, Eastern sands, city centre Geelong
1 Bellarine St, Geelong, (03) 5221 5577
$135 – $155 per night

Organising committee: Craig Sherman, Adam Miller, Julia Kent, Kim Weston, Christopher McAvaney and Adam Cardilini.