参考文献/References:
［1］ Sanger F，Nicklen S，Coulson A R．DNA sequencing with chain-terminating inhibitors［J］．Proceedings of the National Academy of Sciences of the United States of America，1977，74(12)：5463-5467．
［2］ Margulies M， Egholm M， Altman W E， et al．Genome sequencing in microfabricated high-density picolitre reactors［J］．Nature，2005，437(7057)：376-380．
［3］ Kai A．STM and AFM of bio/organic molecules and structures［J］．Surface Science Reports，1996，26(8)： 263-332．
［4］ Hibbs X，Krstic S，Mastrangelo A，et al．The potential and challenges of nanopore sequencing［J］．Nature Biotechnology，2008，26(10)：1146-1153．
［5］ Kahn S D．On the future of genomic data［J］．Science， 2011，331(6018)：728-729．
［6］ Grumbach S，Tahi F．Compression of DNA sequences［C］// In Proceedings of Data Compression Conference． Snowbird(USA)： IEEE Computer Society, 1993：340-350．
［7］ Giancarlo R，Scaturro D，Utro F．Textual data compression in computational biology: asynopsis［J］．Bioinformatics，2009，25(13)：1575-1586．
［8］ Matsumoto T，Sadakane K，Imai H．Biological sequence compression algorithms［C］// Proceedings of Genome Informatics Workshop，Tokyo，2000: 43-52．
［9］ Chen X，Li M，Ma B，et al．DNA compress：fast and effective DNA sequence compression ［J］. Bioinformatics, 2002,18(2)：1696-1698．
［10］ Loewenstern D，Yianilos P N．Significantly lower entropy estimates for natural DNA sequences［J］．Computational Biology，1999，6(1)：125-142．
［11］ Cao M D，Dix T I，Allison L，et al．A simple statistical algorithm for biological sequence compression［C］// In Proceedings of the Conference on Data Compression， Snowbird(USA)：IEEE Computer Society, 2007：43-52．
［12］ Zhang Lixia，Song Hongzhi．Multiple-compression of DNA sequence data［J］．Journal of Computer Applications，2010，30(5)：1379 -1382．(in Chinese)
张丽霞，宋鸿陟．多重压缩DNA序列数据［J］．计算机应用，2007，30(5)：1379-1382．
［13］ Fritz M H Y， Leinonen R， Cochrane G， et al．Efficient storage of high throughput DNA sequencing data using reference-based compression［J］．Genome Research， 2011，21(5)：734-740.
［14］ Jones D，Ruzzo W，Peng X，et al．Compression of next-generation Sequencing reads aided by highly efficient de novo assembly［J］．Nucleic Acids Research，2012， 40(22)：e171．
［15］ Christley S，Lu Y，Li C，et al．Human genomes as email attachments［J］．Bioinformatics，2009，25(2)：274-275．
［16］ Kent W J．BLAT：the BLAST-like alignment tool［J］．Genome Research，2002，12(4)：656-664．
［17］ Altschul S，Gish W，Miller W，et al．Basic local alignment search tool［J］．Journal of Molecular Biology，1990，215(3)：403-410．
［18］ Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores［J］. Genome Research，2008，18(11)：1851-1858．
［19］ Li H，Durbin R．Fast and accurate short read alignment with burrows-wheeler transform［J］．Bioinformatics， 2009，25(14)：1754-1760．
［20］ Brandon M C，Wallace D C， Baldi P．Data structures and compression algorithms for genomic sequence data［J］．Bioinformatics，2009，25(14)：1731-1738．
［21］ Zhu Z，Zhou J，Ji Z，et al．DNA sequence compression using adaptive particle swarm optimization-based memetic algorithm［J］．IEEE Transactions on Evolutionary Computation，2011，15(5)：643-658．
［22］ Korodi G，Tabus I．An efficient normalized maximum likelihood algorithm for DNA sequence compression［J］．ACM Transactions on Information Systems，2005，23(1)：3-34．
［23］ Korodi G，Tabus I．Normalized maximum likelihood model of order-1 for the compression of DNA sequences［C］// Data Compression Conference．Snowbird(USA)：IEEE Computer Society，2007：33-42．
［24］ Kuruppu S，Puglisi S J，Zobel J．Relative Lempel-Ziv compression of genomes for large-scale storage and retrieval［C］// in proceedings of the 17th International Symposium on String Processing and Information Retrieval．Los Cabos：Springer，2010：201-206．
［25］ Kuruppu S，Puglisi S J，Zobel J．Optimized relative Lempel-Ziv compression of genomes［C］// Proceedings of Australasian Computer Science Conference．Perth(Australia)：Australasian Computer Science，2011：91-98．
［26］ Wang C，Zhang D．A novel compression tool for efficient storage of genome resequencing data［J］．Nucleic Acids Research，2011，39(7)：E45-U74．
［27］ Miller J R，Koren S，Sutton G．Assembly algorithms for next generation sequencing data［J］．Genomics，2010， 95(6)：315-327．
［28］ Pevzner P A，Tang H，Waterman M S．An Eulerian path approach to DNA fragment assembly［J］．PNAS，2001， 98(17)：9748-9753．
［29］ Li R Q，Zhu H M，Ruan J，et al．De novo assembly of human genomes with massively parallel short read sequencing［J］．Genome Research，2010，20(2)，265-272．
［30］ Tembe W，Lowey J，Suh E．G-SQZ：compact encoding of genomic sequence and quality data ［J］. Bioinformatics, 2010，26(17)：2192-2194．
［31］ Deorowicz S, Grabowski S. Compression of DNA sequence reads in FASTQ format［J］．Bioinformatics，20 11，27(6)：860-862．
［32］ Popitsch N，Haeseler A V．NGC：lossless and lossy compression of aligned high throughput sequencing data［J］．Nucleic Acids Research，2012，41(1)：e27．
［33］ Kuruppu S S．Compression of Large DNA Databases［D］. Melbourne：Melbourne School of Engineering，2012．
［34］ FerraginaP，Manzini G．Opportunistic data structures with applications［C］// Proceedings of the 41st Annual Symposium on Foundations of Computer Science． Redondo Beach：IEEE Computer Society，2000：390-398．
［35］ Makinen V，Navarro G．Succinct suffix arrays based on run-length encoding［C］// In Proceedings of the 16th Annual Symposium on Combinatorial Pattern Matching．Jeju Island(Korea)：Springer，2005：40-66．
［36］ Grossi R，Vitter J S．Compressed suffix arrays and suffix trees with applications to text indexing and string matching［J］．SIAM Journal on Computing，2005，35(2)：378-407．
［37］ Siren J, Valimaki N, Makinen V, et al. Run-length compressed indexes are superior for highly repetitive sequence collections［C］// String Processing and Information Retrieval．Berlin：Springer，2009：164-175．
［38］ Karkkainen E, Ukkonen. Lempel-Ziv parsing and sublinear- size index structures for string matching［C］// Proceedings of the 3rd South American Workshop on String Processing．Belo Horizonte(Brazil)：World Scientific Publishing Company Incorporated，1996：141-155．
［39］ Kreft S，Navarro G．Self-Indexing based on LZ77［C］// In Proceedings of the 22th Annual Symposium on Combinational Pattern Matching．Palermo(Italy)：Springer, 2011：41-54．
［40］ Bao S，Jiang R，Kwan W，et al．Evaluation of next-generation sequencing software in mapping and assembly［J］．Journal of Human Genetics，2011，56(9)： 406-414．
［41］ SteinL D．The case for cloud computing in genome informatics［J］．Genome Biology，2010，11(5)：207．
［42］ Ansorge W J. Next-generation DNA sequencing techniques［J］．New Biotechnology，2009，25(4)：195-203．
［43］ Horner D S，Pavesi G，Castrignano T，et al．Bioinformatics approaches for genomics and post genomics applications of next generation sequencing［J］．Briefings in Bioinformatics，2010，11(2)：181-197．
［44］ Morozova O，Marra M A．Applications of next-generation sequencing technologies in functional genomics［J］．Genomics，92(5)：255-264．
［45］ Yang X，Charlebois P，Gnerre S，et al．De novo assembly of highly diverse viral populations ［J］. BMC Genomics, 2012，13：475．
相似文献/References:
[1]蔡华利,刘鲁,樊坤,等.基于BPSO的web服务推荐策略[J].深圳大学学报理工版,2010,27(1):49.
CAI Hua-li,LIU Lu,FAN Kun,et al.Web services recommendation based on BPSO[J].Journal of Shenzhen University Science and Engineering,2010,27(No.4(331-440)):49.
[2]张滇,明仲,刘刚,等.基于传感器节点的无线接收信号强度研究（英文）[J].深圳大学学报理工版,2014,31(1):63.[doi:10.3724/SP.J.1249.2014.01063]
Zhang Dian,Ming Zhong,Liu Gang,et al.An empirical study of radio signal strength in sensor networks using MICA2 nodes[J].Journal of Shenzhen University Science and Engineering,2014,31(No.4(331-440)):63.[doi:10.3724/SP.J.1249.2014.01063]
[3]廖日军,李雄军,徐健杰,等.Arnold变换在二值图像置乱应用中若干问题讨论[J].深圳大学学报理工版,2015,32(4):428.[doi:10.3724/SP.J.1249.2015.04428]
Liao Rijun,Li Xiongjun,Xu Jianjie,et al.Discussions on applications of Arnold transformation in binary image scrambling[J].Journal of Shenzhen University Science and Engineering,2015,32(No.4(331-440)):428.[doi:10.3724/SP.J.1249.2015.04428]
[4]李雄军,廖日军,李金龙,等.图像Arnold变换中的准对称性问题与半周期现象[J].深圳大学学报理工版,2015,32(6):551.[doi:10.3724/SP.J.1249.2015.06551]
Li Xiongjun,Liao Rijun,Li Jinlong,et al.Quasi-symmetry and the half-cycle phenomenon in scrambling degrees for images with pixel locations scrambled by Arnold transformation[J].Journal of Shenzhen University Science and Engineering,2015,32(No.4(331-440)):551.[doi:10.3724/SP.J.1249.2015.06551]
[5]柴变芳,曹欣雨,魏春丽,等.一种主动半监督大规模网络结构发现算法[J].深圳大学学报理工版,2020,37(3):243.[doi:10.3724/SP.J.1249.2020.03243]
CHAI Bianfang,CAO Xinyu,WEI Chunli,et al.An active semi-supervised structure exploring algorithm for large networks[J].Journal of Shenzhen University Science and Engineering,2020,37(No.4(331-440)):243.[doi:10.3724/SP.J.1249.2020.03243]
[6]刘朝斌,孙雪,刘剑,等.基于物联网的高校校园智能安防建设探索[J].深圳大学学报理工版,2020,37(增刊1):128.[doi:10.3724/SP.J.1249.2020.99128]
LIU Chaobin,SUN Xue,LIU Jian,et al.Campus intelligent security construction based on internet of things[J].Journal of Shenzhen University Science and Engineering,2020,37(No.4(331-440)):128.[doi:10.3724/SP.J.1249.2020.99128]
[7]杨阳.高校大数据平台的规划设计与实现[J].深圳大学学报理工版,2020,37(增刊1):146.[doi:10.3724/SP.J.1249.2020.99146]
YANG Yang.Design and implementation of big data platform in colleges[J].Journal of Shenzhen University Science and Engineering,2020,37(No.4(331-440)):146.[doi:10.3724/SP.J.1249.2020.99146]
[8]龚黎旰,顾坤,明心铭,等.基于校园一卡通大数据的高校学生消费行为分析[J].深圳大学学报理工版,2020,37(增刊1):150.[doi:10.3724/SP.J.1249.2020.99150]
GONG Ligan,GU Kun,MING Xinming,et al.Analysis of college students’ consumption behavior based on campus card data[J].Journal of Shenzhen University Science and Engineering,2020,37(No.4(331-440)):150.[doi:10.3724/SP.J.1249.2020.99150]
[9]林晓玲,王志强,等.基于多约束场景的BFO-ACO漫游路径规划[J].深圳大学学报理工版,2022,39(4):463.[doi:10.3724/SP.J.1249.2022.04463]
LIN Xiaoling,WANG Zhiqiang,GUO Yanyan,et al.BFO-ACO roaming path planning based on multi-constraint scenarios[J].Journal of Shenzhen University Science and Engineering,2022,39(No.4(331-440)):463.[doi:10.3724/SP.J.1249.2022.04463]
[10]蔡伊娜,陈新,覃志武,等.基于改进CDC的实验原始记录匹配算法[J].深圳大学学报理工版,2022,39(5):509.[doi:10.3724/SP.J.1249.2022.05509]
CAI Yina,CHEN Xin,QIN Zhiwu,et al.An algorithm for matching original experimental records based on improved CDC[J].Journal of Shenzhen University Science and Engineering,2022,39(No.4(331-440)):509.[doi:10.3724/SP.J.1249.2022.05509]