CUDA-FRESCO: Frequency-Based RE-Sequencing Tool Based on CO-clustering Segmentation by GPU

Recently, many new next-generation sequencing techniques have been proposed. These techniques can produce lot of short reads rapidly. Hence, a number of tools have been developed to map these short reads to the genome. However, with more and more reads sequenced and the length of reads increases, these tools require high memory usage and huge computational cost and are also impractical for utilization. As the GPU has become increasingly more powerful and ubiquitous, many scientific applications have been implemented to enhance the computational performance on GPU platform. In this paper, we proposed a method, CUDA-FRESCO, to map the short reads to the genome by using CUDA on GPU platform. The experimental results present that CUDA-FRESCO can achieve dramatic speed up than other tools. CUDA-FRESCO can be alternative tool for biologists to map the short reads fast.