BarraCUDA
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Application data |
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| Created by | Bill Langdon, Petr Klus, Simon Lam, Giles Yeo, Brian Lam |
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| Biological application domain(s) | Sequence analysis |
| Principal bioinformatics method(s) | Read mapping, Sequence alignment |
| Technology | Illumina, ABI SOLiD |
| Created at | University of Cambridge and University College London |
| Maintained? | Yes |
| Input format(s) | .fastq/.fq, .fq.gz, .bam |
| Output format(s) | SAM |
| Software features | Gapped and ungapped alignment, paired-end mapping, GPGPU, parallel execution |
| Programming language(s) | C, C++, CUDA |
| Software libraries | CUDA 6.5, Zlib |
| Licence | GPLv3, MIT |
| Operating system(s) | Linux |
Summary: Barracuda is a high-speed sequence aligner based on BWA and uses the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by the next-generation sequencers.
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Description
With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters.
Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput.
BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available from http://seqbarracuda.sf.net.
Links
References
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