Computer Science ›› 2018, Vol. 45 ›› Issue (12): 308-312.doi: 10.11896/j.issn.1002-137X.2018.12.049
• Interdiscipline & Frontier • Previous Articles
WU Si-wen, LI Jing, ZHANG Shao-qiang
CLC Number:
[1]YU A M.Research on the sugar and terpenoid metabolism du-ring the AmomumvillosumLour.fruit development using RNA-Seq [D].Guangzhou:Guangzhou University of Chinese Medicine,2014.(in Chinese) 于安民.基于RNA-Seq的阳春砂果实发育过程中糖和萜类代谢的研究[D].广州:广州中医药大学,2014. [2]QI Y X,LIU Y B,RONG W H.RNA-Seq and its applications:a new technology for transcriptome [J].Herditas,2011,33 (11):1191-1202.(in Chinese) 祁云霞,刘永斌,荣威恒.转录组研究新技术:RNA-Seq及其应用[J].遗传,2011,33(11):1191-1202. [3]LU Z Y.Research on assembly algorithm for next new generation sequencing technology [D].Nanjing:Southeast University,2011.(in Chinese) 卢志远.面向新一代测序技术的拼接算法研究[D].南京:东南大学,2011. [4]PERTEA G.Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching du-ring cell differentiation [J].Nature Biotechnology,2010,28(5):511-515. [5]MINGFU S,CARL K.Accurate assembly of transcripts through phase-preserving graph decomposition [J].Nature Biotechnology,2017,35(12):1167-1169. [6]LIU J T,YU T,JIANG T,et al.TransComb:genome-guided transcriptome assembly via combing junctions in splicing graphs [J].Genome Biology,2016,17(1):213. [7]PERTEA M,PERTEA GM,ANTONESCU C M,et al.StringTie enables improved reconstruction of a transcriptome from RNA-Seq reads [J].Nature Biotechnology,2015,33(3):290-295. [8]MARETTY L,SIBBESEN J A,KROGH A,et al.Bayesiantranscriptome assembly [J].Genome Biology,2014,15(10):501. [9]SCHULZ M H,ZERBINO D R,Vingron M,et al.Oases:robust de novo RNA-seq assembly across the dynamic range of expression levels [J].Bioinformatics,2012,28(8):1086-1092. [10]XIE Y,WU G,TANG J,et al.SOAPdenovo-Trans:de novotranscriptome assembly with short RNA-Seq reads [J].Bioinformatics,2014,30(12):1660. [11]PENG Y,LEUNG H C,YIU S M,et al.IDBA-Tran:a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels [J].Bioinformatics,2013,29(13):326-334. [12]GRABHERR M G,HAAS B J,YASSOUR M,et al.Trinity:reconstructing a full-length transcriptome without a genome from RNA-Seq data [J].Nature Biotechnology,2011,29(7):644-652. [13]CHANG Z.De novo transcriptome assembly from RNA-Seq[D].Jinan:Shandong University,2014.(in Chinese) 常征.基于RNA测序技术的转录组从头拼接算法研究[D].济南:山东大学,2014. [14]ZHENG C,LI G,LIU J,et al.Bridger:a new framework for de novo transcriptome assembly using RNA-seq data [J].Genome Biology,2015,16(1):30. [15]XIONG X J.Introduction to NCBI’s SRA database [J].Chemistry of Life,2010(6):959-963.(in Chinese) 熊筱晶.NCBI高通量测序数据库SRA介绍[J].生命的化学,2010(6):959-963. |
[1] | GUO Mao-zu, YANG Shuai, ZHAO Ling-ling. Transcriptome Analysis Method Based on RNA-Seq [J]. Computer Science, 2020, 47(11A): 35-39. |
[2] | DONG Gai-fang, FU Xue-liang and LI Hong-hui. Improvement of Multiple Sequence Center Star Method and Its Parallelization in Spark [J]. Computer Science, 2017, 44(10): 55-58. |
[3] | WANG Lei ,ZHANG Zu-Ping, CHEN Jian-Er (School of Information Science & Engineering,Central South University,Changsha 410083). [J]. Computer Science, 2006, 33(7): 164-166. |
|