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This GitHub repo has been setup to help foster a more sustainable collaborative environment in which the workshop content can be developed and refined. To facilitate this we are:

  • Porting all the documentation over to LaTeX - easy to version control and easier to collaborate on content. Easy to get consistent styling and can (will) be able to parse out code (listings) from within the LaTeX docs for easy automated testing of the code.
  • Developing the Bioinformatics Training Platform (BTP), an Ubuntu based OS containing features to help develop and deliver hands-on bioinformatics training in a more collaborative fashion. In addition, we hope to provide a framework through which people can shared and access workshop content as well as configure the BTP quickly and easily for such a workshop. This is still in development as a proof-of-concept.


For information on writing the handouts in LaTeX see the file and see the downloads page for up-to-date PDF versions of the workshop handouts.

Creative Commons License

The documentation associated with this workshop are released under the Creative Commons Attribution 3.0 Unported License. For a summary of what this means, please see:

Course Overview

A 2-day hands-on Next Generation Sequencing (NGS) Workshop developed by Bioplatforms Australia (BPA), the Commonwealth Scientific and Industrial Research Organisation (CSIRO), EMBL-Australia and the European Bioinformatics Institute.

This course was designed to familiarise participants with NGS data analysis and provide hands-on computational experience in analysing NGS data using common analytical workflows for, ChIP-seq, RNASeq 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 statistical analysis.

Target Audience

This 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.


Because places are limited (approx. 30 places), registration is via a selection process. Therefore applicants should be aware that, in order to be considered for a place on this course, they MUST complete an application form.

Computer Lab Setup

This workshop has been designed to be run on VM's on Australia's NeCTAR Research Cloud. Trainees, then use the NoMachine NX Client to provide a remote desktop like connection to their own dedicated VM for the duration of the workshop.

This approach means that the workshop can be delivered in a road-show style form around Australia, without being limited by local computational resources. The level of IT support, required of the local hosting institution, is minimal and only requires the installation of the NoMachine NX Client and SSH firewall access over port 22 TCP.

We has also developed an Ubuntu 12.04 Image, based on Cloud BioLinux, for the purpose of running this workshop. alpha