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Harnessing the power of supercomputing to map plant genomes

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Case study

Harnessing the power of supercomputing to map plant genomes

The genome of a plant is just as complicated as that of a human, and its analysis requires enormous amounts of computing power, says Dr Yuan Fu, post-doctoral research assistant in plant bioinformatics at Aberystwyth University.

Fu is part of the Biotechnology and Biological Science (BBSRC)-funded Cores Strategic Programme (CSP) in Grasslands and Crops for Challenging Environments project team, studying the genome of important forage, amenity and bio-energy grasses, including perennial ryegrass (Lolium perenne). Through funding from the Global Challenges Research Fund, Fu and colleagues have been applying their expertise in ryegrass genomics to improve understanding of the vast range of genetic resources that are available for this species.

“We have sequenced 200 ryegrass genomes, sampled from 10 separate populations distributed across southern and eastern Europe, and through analysing this dataset we want to build up a picture of the population structure to figure out the genetic relationships between them, going back many years. We really need a lot of storage just for our sequences even before we begin to analyse our data, and in fact that’s the first thing that Supercomputing Wales offered us,” Fu says.

The data analysis needed to find relationships between the plants is complex and time consuming, she says.

“You’ve got all these data and you need to clean them up, and then we start to call the SNPs, the single nucleotide polymorphisms.

“We use machine learning algorithms to predict the structure of the ryegrass genome first, and that requires a lot of predictions and recalculating round by round, and then we use Bayesian models to check whether we have found a real SNP or just a random sequencing error – is it meaningful or not?” says Fu.

“But luckily with Supercomputing Wales we can apply for multiple cores, say, 120 cores and work 120 times faster,” she says. “We just throw them into Supercomputing Wales and they run for you.”

The support team at Supercomputing Wales has always been helpful when it comes to installing and running the project’s software on the system, and fast to provide storage and compute time.

“You have to ask in advance for storage and time, but they are fast. They have a ticket system to request what you need, or ask about a problem, and there’s also a meeting every week with other users where we can discuss any issues and help one another,” Fu says.

Having worked with other HPC facilities internationally, Fu is pleased with how well Supercomputing Wales operates.

“It’s organised in a very good and efficient way. This one is the best for me!”

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