基于Pthreads的并行DSRC压缩算法设计与实现

doi:10.11896/j.issn.1002-137X.2015.01.021

计算机科学 ›› 2015, Vol. 42 ›› Issue (1): 90-91.doi: 10.11896/j.issn.1002-137X.2015.01.021

• 2013年全国理论计算机科学学术年会 • 上一篇下一篇

基于Pthreads的并行DSRC压缩算法设计与实现

詹科,张云泉,王婷,郑晶晶,张鹏

中国科学院软件研究所并行软件与计算科学实验室北京100190,中国科学院计算技术研究所计算机体系结构国家重点实验室北京100190,中国科学院软件研究所并行软件与计算科学实验室北京100190;广州中国科学院软件应用技术研究所广州511458,中国科学院软件研究所并行软件与计算科学实验室北京100190,中国科学院软件研究所并行软件与计算科学实验室北京100190

出版日期:2018-11-14 发布日期:2018-11-14
基金资助:
本文受国家“八六三”高技术研究发展计划基金(2012AA010903),国家自然科学基金项目(61170075,61133005,61272136,3),广州市云计算技术研发与产业化专项资助

Design and Implementation of Parallel DSRC Compression Algorithm Based on Pthreads

ZHAN Ke, ZHANG Yun-quan, WANG Ting, ZHENG Jing-jing and ZHANG Peng

Online:2018-11-14 Published:2018-11-14

摘要/Abstract

摘要： 高通量测序仪产生大量的DNA数据,FASTQ是被广泛使用的存储DNA数据的数据格式。对FASTQ格式的数据进行压缩处理,能有效地节省存储空间。DSRC算法具有压缩比高的优点,因此对DSRC算法进行并行能提高压缩FASTQ格式的DNA数据的效率。基于Pthreads,实现了并行DSRC算法。测试结果表明,当使用4线程时加速比达到3.5。

关键词: FASTQ,数据压缩,DSRC,Pthreads

Abstract: With the development of high throughput sequencing technology,large volumes of DNA data are being genera-ted.The FASTQ format is widely used to store DNA sequence.If the DNA sequence reads in FASTQ format can be compressed,the storage space will be saved efficiently.One of the DSRC advantages is the high compression ratio,therefore parallel DSRC algorithm will increase the efficiency of compressing the DNA sequence reads in FASTQ format.We implemented the parallel DSRC algorithm based on Pthreads,and the experimental results indicate that the para-llel DSRC algorithm gets 3.5 speedup when four threads are used.

Key words: FASTQ,Data compression,DSRC,Pthreads

詹科,张云泉,王婷,郑晶晶,张鹏. 基于Pthreads的并行DSRC压缩算法设计与实现[J]. 计算机科学, 2015, 42(1): 90-91. https://doi.org/10.11896/j.issn.1002-137X.2015.01.021

ZHAN Ke, ZHANG Yun-quan, WANG Ting, ZHENG Jing-jing and ZHANG Peng. Design and Implementation of Parallel DSRC Compression Algorithm Based on Pthreads[J]. Computer Science, 2015, 42(1): 90-91. https://doi.org/10.11896/j.issn.1002-137X.2015.01.021

参考文献

[1] Tembe W,et al.G-SQZ:compact encoding of genomic sequence and quality data[J].Bioinformatics,2010,26(17):2192-2194
[2] Jones D C,et al.Compression of next-generation sequencingreads aided by highly efficient de novo assembly[J].Nucleic Acids Res.,2012,40(22),e171
[3] Deorowicz S,et al.Compression of DNA sequence reads inFASTQ format[J].Bioinformatics,2011,27(6):860-862
[4] https://computing.llnl.gov/tutorials/pthreads/#Abstract
[5] http://www.1000genomes.org/

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基于Pthreads的并行DSRC压缩算法设计与实现

Design and Implementation of Parallel DSRC Compression Algorithm Based on Pthreads

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