Scientists use SGI supercomputers to sequence new genomes

Researchers at the Genome Analysis Centre (TGAC) have managed to sequence a number of genomes for the first time thanks to supercomputers from SGI.


Researchers at the Genome Analysis Centre (TGAC) have managed to sequence a number of genomes for the first time thanks to supercomputers from SGI.

The rapid processing power provided by three supercomputers allowed the centre to be at the forefront of research into ash dieback disease last year.

It has also allowed the centre to be the first to sequence certain genomes, such as for the rubber tree and certain rice and wheat genomes.

The team was able to sequence genomes of the fungus responsible for the spread of ash dieback in just two days, whereas previously it would have taken over a week, according to Bernardo Clavijo, one of the bioinformaticians at TGAC.

Moving from a ‘Beowolf’ computer cluster to three of SGI’s ‘UV’ supercomputers has increased the computing power the team has as its disposal by more than ten times over, TGAC’s science computing team leader Paul Fretter explained.

He said: “We wanted one company to provide hardware, interconnect, a customised OS [operating system] if necessary, systems and software support. The only firm that could fit the bill was SGI.”

TGAC is based in Norwich and has just over 50 staff. Half of the employees there work in bioinformatics interpreting, assembling and analysing datasets generated from sequencers, which rely on high-performance compute capability.

Clavijo explained the importance of increased computing speeds to the research team, particularly in the case of the ash dieback project.

He said: “The first and best thing is that it runs a lot faster, so that gives us an edge on times. One of the recent projects we’ve been involved in is the ash dieback outbreak. In that case, it was key to produce results accurately and fast.

“Having the SGI UV 100 machines allows us to try lots of different combinations to get the best results in a couple of days. These sorts of analysis would not have been possible previously…processing was around one or two weeks.”

Since then TGAC has sequenced genomic data from ‘Tree 35’, a survivor of the Danish ash dieback epidemic. The data is vitally important as it provides insight into why some trees can survive infection.

The genetic insights could eventually be used to cross ‘Tree 35’ with existing stock from the UK’s native ash population, enabling depleted woodland to be restocked, TGAC explained.

SGI provides supercomputers to a wide range of academic institutions around the world, including the Crick Institute, the University of Arizona, Kyoto University and the National University of Singapore.

In June the UK Atomic Weapons Establishment (AWE) announced that it had deployed three SGI supercomputers to improve the development and maintenance of nuclear warheads.

The company also works with U.S. federal government departments, NASDAQ, YouTube and NASA.