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Assembling genomes

22 February 2016
Koala Genome - Ramaciotti Centre for Genomics

The work at the Ramaciotti Centre for Genomics at UNSW involves a very wide net of collaborators and Intersect's high performance computing (HPC) facilities underpin all their genome assembly efforts.  

Professor Marc Wilkins (Director of the Centre) and other genetic researchers use HPC to generate and analyse genomics and transcriptomics data.  The generation of these data reveals in detail the nature of the genetic material inside cells and how genes are expressed and regulated, highlighting the fundamental properties and processes drive the rapidly growing field of genetics, a major international endeavour.

The ‘next generation’ sequencing machines, installed at the Centre generate massive datasets comprising over two million sequence reads per run. The assembly of genomes from these data requires each sequence to be compared to each other sequence (four thousand billion comparisons).  Once genomes are assembled, they are analysed to find coding genes.  The coding genes are finally identified by comparing them (e.g. the 22,000 or so in a mammalian genome) with the millions of all known genes in databases with alignment search tools.

Recent projects include the sequencing, assembly and analysis of the koala genome, the Australian black field cricket, the Queensland fruit fly, five isolates of drug resistant Cryptococcus and eight isolates of pathogenic Campylobacter.  The generation of new genome sequences is extremely compute intensive, and is only possible through access to HPC.