CUDA-EC is a fast parallel sequence error correction tool for short reads. It corrects sequencing errors in high-throughput short-read (HTSR) data and accelerates HTSR by taking advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs. Error correction is a preprocessing step for many DNA fragment assembly tools and is very useful for the new high-throughput sequencing machines.

Download and Installation

• Download CUDA-EC
• Installation instructions and user guide are also in the software download

Benchmark Data

CUDA-EC running on one Tesla C1060 GPU is up to 20x faster than Euler-SR running on a x86 CPU. This cuts compute time from minutes on CPUs to seconds using GPUs. The data in the chart below are error rates of 1%, 2%, and 3% denoted by A1, A2, A3 and so on for 5 different reference genomes.

Technical Papers

• "Accelerating Error Correction in High-Throughput Short-Read DNA Sequencing Data with CUDA , H. Shi et al: International Workshop on High Performance Computational Biology (HiCOMB 2009)
• "A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-enabled Graphics Hardware, H. Shi et al: to appear in Journal of Computational Biology
• More publications on accelerating bio-informatics applications using GPUs

Discussion Forums

• GPU computing communities on GPUcomputing.net

The Tesla Bio Workbench applications can be deployed on GPU-based desktop personal supercomputers or in data center solutions. Built on the revolutionary massively parallel CUDA architecture, these solutions are designed to accelerate the pace of computational science.

RECOMMENDED HARDWARE CONFIGURATION

WORKSTATION SOLUTIONS TESLA PERSONAL SUPERCOMPUTER For personal supercomputing at your desk Learn more > Where to buy >		DATA CENTER SOLUTIONS TESLA GPU COMPUTING CLUSTERS For computing with large-scale installations Learn more > Where to buy >