GPU-Accelerated Short Read Aligner

January 17, 2012

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Researchers from the University of Cambridge and the University College Cork have released BarraCUDA, a GPU-accelerated short read DNA sequence alignment software based on BWA.

The team used Nvidia's Compute Unified Device Architecture (CUDA) to develop the software on a GPU. BarraCUDA demonstrated a throughput six times the speed of a CPU core for gapped alignment and even faster when gap opening is disabled.

They describe BarraCUDA in BMC Research Notes.

According to the team, when it comes to implementing alignment software, multiple GPUs scale better than CPUs. They write that "a normal computer can easily take up 4 GPUs, meaning that using this test library as an example, a single-end alignment can be done in 5 min, which is twice the speed of a high-end 12-core workstation. Using 8X GPU, we can achieve an alignment speed 3X faster than a traditional computing node with 12 CPU cores, making GPU nodes a more favourable option, in terms of HPC environment, than using those with CPUs."

BarraCUDA can be downloaded here.

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