Wednesday, 18 January 2012
BarraCUDA is a GPU-accelerated short read DNA sequence alignment software based on Burrows-Wheeler Aligner (BWA).
Researchers from the University of Cambridge and the University College Corkused Nvidia's Compute Unified Device Architecture (CUDA) have designed the software to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. Quite impressively BarraCUDA demonstrated a throughput six times the speed of a CPU core for gapped alignment and even faster when gap opening is disabled. Mapping accuracy is not compromised by using GPUs.
Notably many modern supercomputers (including the Chinese Tianhe-1A, the second most powerful system in the world) also contain multiple GPU nodes on top of traditional nodes with CPUs to take advantage to the parallel computing capability of GPUs