Intensive training in Cancer Genomics and the Genome Analysis Tool Kit in Melbourne
Two of the latest instalments of Bioplatforms Australia training workshops have been held in Melbourne and Sydney in February. The GATK Best Practice course brought the Broad Institute’s Geraldine Van der Auwera to the University of New South Wales and the University of Melbourne. A new 3-day Cancer Genomics workshop was run in the Melbourne biomedical precinct, after its successful Canberra rollout in late 2015.
GATK, or the Genome Analysis Toolkit, is a widely used software package developed at the Broad Institute, USA, to perform variant discovery analysis on high-throughput sequencing data. The workshop provided an opportunity for participants from Brisbane, Canberra and Melbourne to learn directly from a GATK developer during the 2-day program of talks and hands-on labs. Staff from EMBL Australia Bioinformatics Resource (BRAEMBL) set up virtual machines equipped with an array of tools and software so the workshop would run smoothly on the Genomics Virtual Laboratory. The GVL instance proved to be a perfect way to streamline the training in a stable environment regardless of the location. A group of experienced bioinformaticians from around the country also attended the workshops and a supplemental training and content development event, including 3 BRAEMBL staff members who will lead future workshops around Australia.
This workshop was followed by a specialist Cancer Genomics workshop that was attended by 17 researchers already working in the field, many of them from Peter MacCallum Cancer Centre. In collaboration with EMBL-EBI, UK, the workshop was developed by experts from JCSMR, QIMR Berghnofer, BRAEMBL, CMRI, Garvan Institute and AGRF.
To assist with the inaugural workshop at the Australian National University in Canberra, Bioplatforms Australia brought in Mathieu Bourgey from McGill University and Genome Quebec. The workshop provides an introduction to cancer genomics analytical pipelines for single nucleotide variations (SNV), copy number variations (CNV) and structural variations (SV) using a mixture of lectures, hands-on practical sessions and open discussions, and will be run in other states in the future.