CUDA-FRESCO: Frequency-based RE-sequencing tool based on CO-clustering segmentation by GPU

Chun Yuan Lin*, Chuan Yi Tang, Sheng Ta Li, Yaw Ling Lin, Che Lun Hung

*此作品的通信作者

研究成果: Conference contribution同行評審

2 引文 斯高帕斯(Scopus)

摘要

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.

原文English
主出版物標題Proc.- 2011 IEEE International Conference on HPCC 2011 - 2011 IEEE International Workshop on FTDCS 2011 - Workshops of the 2011 Int. Conf. on UIC 2011- Workshops of the 2011 Int. Conf. ATC 2011
頁面857-862
頁數6
DOIs
出版狀態Published - 2011
事件13th IEEE International Workshop on FTDCS 2011, the 8th International Conference on ATC 2011, the 8th International Conference on UIC 2011 and the 13th IEEE International Conference on HPCC 2011 - Banff, AB, Canada
持續時間: 2 9月 20114 9月 2011

出版系列

名字Proc.- 2011 IEEE International Conference on HPCC 2011 - 2011 IEEE International Workshop on FTDCS 2011 -Workshops of the 2011 Int. Conf. on UIC 2011- Workshops of the 2011 Int. Conf. ATC 2011

Conference

Conference13th IEEE International Workshop on FTDCS 2011, the 8th International Conference on ATC 2011, the 8th International Conference on UIC 2011 and the 13th IEEE International Conference on HPCC 2011
國家/地區Canada
城市Banff, AB
期間2/09/114/09/11

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