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Next Generation Sequencing Workshop 2012

Friday, 01 June 2012 00:00

Bioplatforms Australia, EMBL-EBI and CSIRO joint Hands-on Training for Analysis of Next Generation Sequence Data.

This course is designed to familiarise participants with next Generation Sequence data analysis and to provide hands-on computational experience in analysis of NGS data using common analytical approaches for ChIP-seq, RNA-Seq data and de novo genome assembly.

Course content

The course covers data analysis of RNA-Seq and ChIP-Seq experiments and de novo genome assembly of small genomes. Topics will include: data quality, alignment, data handling and visualisation, region identification, transcriptome analysis and basis statistical analysis.

Target Audience

The practical 2 day hands-on course is designed for bench biologists, PhD students or early career postdoctoral researchers with no or basic bioinformatics experience who are planning or currently using NGS approaches in their research area.


  • Dr Matthais Haime, EMBL-EBI, UK
  • Dr Remco Loos, EMBL-EBI, UK
  • Dr Myrto Kostadima, EMBL-EBI, UK
  • Dr Sean McWilliam, CSIRO, AUS
  • Dr Sonika Tyagi, AGRF, AUS
  • Dr Nathan Watson-Haigh, AWRI, AUS
  • Dr Sean Li, CSIRO, AUS
  • Dr Konsta Duesing, CSIRO, AUS
  • Dr Paula Moolhuizen, CCG, AUS
  • Dr Nandan Despande, UNSW, AUS

Workshop Dates

City Location Date
Melbourne Monash University 12-13 July, 2012
Sydney University of NSW 16-17 July
Adelaide, Brisbane, Perth, Hobart TBC TBC

Provisional Program

Day 1 - Introduction to NGS and ChIP-seq data analysis

Time Topic
09:40 - 10:30 Next generation sequencing overview
10:30 - 10:50 Morning Tea
10:50 - 12:25 Practical: NGS quality control and sequence alignment
12:25 - 13:10 Lunch
13:10 - 14:00 Introduction to ChIP-seq
14:00 - 15:30 Practical: ChIP-seq analysis - peak calling and annotation
15:30 - 15:50 Afternoon Tea
15:50 - 16:40 Practical: ChIP-seq analysis - motif analysis
16:40 - 17:30 Wrap up of day 1 and discussions

Day 2 - Introduction to RNA-seq and de novo genome assembly

Time Topic
09:00 - 09:10 Welcome and introductions to Day 2
09:10 - 09:40 Introduction to RNA-seq
09:40 - 10:15 Practical: alignment and slice junction identification
10:15 - 10:40 Practical: transcriptome assembly
10:40 - 11:05 Morning Tea
11:05 - 12:30 Practical: differential expression analysis
12:30 - 13:15 Lunch
13:15 - 13:45 Introduction to de novo assembly
13:45 - 15:30 Practical: de novo assembly using velvet (part 1 and 2)
15:30 - 15:45 Afternoon tea
15:45 - 16:45 Practical: de novo assembly using velvet (part 3)
16:45 - 17:05 Review and discussion of Velvet de novo assembly exercises
17:05 - 17:30 General course discussion and feedback survey completion

Registration and Payment
Due to the practical component of this course places are limited. The closing date for application is 27 June (12:00 noon AEST).

Successful applicants will be notified by email by 29th June this will include instructions for course payment. Registration will be via a selection process therefore applicants should be aware that, in order to be considered for place on this course, they MUST complete the application page. Items marked * are mandatory. Incomplete registrations will not be processed. The course cost is $150 and includes morning and afternoon tea and lunches.

Registration Closed


If you are unable to apply online please download the application form and email the completed form to This e-mail address is being protected from spambots. You need JavaScript enabled to view it

For further information contact Catherine Shang This e-mail address is being protected from spambots. You need JavaScript enabled to view it .


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