De Novo Assembly

What this course covers

The de novo assembly workshop will provide an introduction to de novo assembly, with hands on exercises followed by in-depth analysis of the key steps in the process. It will cover aspects such as quality control and pre-processing of datasets, generation and evaluation of first pass assemblies, assembly improvement and scaffolding. Practical exercises will be performed on small-scale real datasets, and will include best practices.

These workshops will consist of a mixture of conceptual lectures, methodological lectures and hands on sessions, as well as group activities. The participants will gain first-hand experience and understanding on NGS assembly, working with the assistance of the training, troubleshooting small problems, and reviewing the results. These workshops have been developed in close collaboration with The Genome Analysis Centre (TGAC), Norwich, UK.

Learning objectives

By the end of the course participants will be able to:

  • To explain the process of genome assembly: apply experimental design and pipelines for the novo assembly.
  • Perform QC, a simple genome assembly, and optimise the parameters affecting the assembly
  • assess and validate the assembly using meaningful metrics

Target Audience

The de novo assembly workshops have been designed for bench scientists who have a specific interest in de novo assembly analysis pipelines. The workshop assumes that attendees have a general understanding of NGS technology. No prior experience with the command line is required, but a familiarity will be useful.

 

Scientific Co-ordinator

Trainers

  • Paul Berkman, CSIRO
  • Zhiliang Chen, SBI
  • Lien Le, BRAEMBL
  • Sean McWilliam, CSIRO
  • Philippe Moncuquet, CSIRO
  • Torsten Seemann, VLSCI
  • Sonika Tyagi, AGRF

International Trainers

  • Bernardo Clavijo, TGAC (TBC)

Workshop Co-ordinators

Workshop Dates

City Location Date Workshop Costs
Brisbane University of Queensland 25th November 2015 $450 (Including GST)

Bioplatforms Australia and CSIRO will also be hosting a de novo assembly workshop at the University of Melbourne on the 30th-2nd of December 2015. For more information please visit www.bioplatforms.com/denovo-2015-melbourne/

Draft Program

For a draft program please click here

Registration and Payment

Workshop places are limited due to the significant practical component of this workshop. To manage high demand, all workshop applicants are subject to a selection process and must complete the online application.

The application period closes 2nd November 2015. Successful applicants will be notified no later than 5th November 2015.

The workshop fee of $450.00 (including GST) covers course material, computer access, lunch and refreshments. If you are unable to apply online please email Katherine Champ at kchamp@bioplatforms.com.

If you are unable to apply online advise Katherine Champ, kchamp@bioplatforms.com

Contact

For further information contact Katherine Champ (kchamp@bioplatforms.com) or Annette McGrath (annette.mcgrath@csiro.au).

Here you can create the content that will be used within the module.

Training Updates

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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 kchamp@bioplatforms.com.
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