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

doi:10.1109/HPCC.2011.122

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

^*Corresponding author for this work

Clinical Informatics and Medical Statistics Research Center

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

2 Scopus citations

Abstract

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.

Original language	English
Title of host publication	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
Pages	857-862
Number of pages	6
DOIs	https://doi.org/10.1109/HPCC.2011.122
State	Published - 2011
Event	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 Duration: 02 09 2011 → 04 09 2011

Publication series

Name	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

Conference	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
Country/Territory	Canada
City	Banff, AB
Period	02/09/11 → 04/09/11

Keywords

GPU
New sequencing techniques
approximate string matching
parallel computing
pattern matching

Access to Document

10.1109/HPCC.2011.122

Cite this

Lin, C. Y., Tang, C. Y., Li, S. T., Lin, Y. L., & Hung, C. L. (2011). CUDA-FRESCO: Frequency-based RE-sequencing tool based on CO-clustering segmentation by GPU. In 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 (pp. 857-862). Article 6063088 (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). https://doi.org/10.1109/HPCC.2011.122

Lin, Chun Yuan ; Tang, Chuan Yi ; Li, Sheng Ta et al. / CUDA-FRESCO : Frequency-based RE-sequencing tool based on CO-clustering segmentation by GPU. 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. 2011. pp. 857-862 (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).

@inproceedings{598528b9b8ab4c7083ecaae45caa878b,

title = "CUDA-FRESCO: Frequency-based RE-sequencing tool based on CO-clustering segmentation by GPU",

abstract = "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.",

keywords = "GPU, New sequencing techniques, approximate string matching, parallel computing, pattern matching",

author = "Lin, {Chun Yuan} and Tang, {Chuan Yi} and Li, {Sheng Ta} and Lin, {Yaw Ling} and Hung, {Che Lun}",

year = "2011",

doi = "10.1109/HPCC.2011.122",

language = "英语",

isbn = "9780769545387",

series = "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",

pages = "857--862",

booktitle = "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",

note = "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 ; Conference date: 02-09-2011 Through 04-09-2011",

}

Lin, CY, Tang, CY, Li, ST, Lin, YL & Hung, CL 2011, CUDA-FRESCO: Frequency-based RE-sequencing tool based on CO-clustering segmentation by GPU. in 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., 6063088, 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, pp. 857-862, 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, 02/09/11. https://doi.org/10.1109/HPCC.2011.122

CUDA-FRESCO: Frequency-based RE-sequencing tool based on CO-clustering segmentation by GPU. / Lin, Chun Yuan; Tang, Chuan Yi; Li, Sheng Ta et al.
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. 2011. p. 857-862 6063088 (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).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AU - Lin, Chun Yuan

AU - Tang, Chuan Yi

AU - Li, Sheng Ta

AU - Lin, Yaw Ling

AU - Hung, Che Lun

PY - 2011

Y1 - 2011

N2 - 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.

AB - 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.

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KW - New sequencing techniques

KW - approximate string matching

KW - parallel computing

KW - pattern matching

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Lin CY, Tang CY, Li ST, Lin YL, Hung CL. CUDA-FRESCO: Frequency-based RE-sequencing tool based on CO-clustering segmentation by GPU. In 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. 2011. p. 857-862. 6063088. (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). doi: 10.1109/HPCC.2011.122

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

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Keywords

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