Literature DB >> 11997349

RePS: a sequence assembler that masks exact repeats identified from the shotgun data.

Jun Wang1, Gane Ka-Shu Wong, Peixiang Ni, Yujun Han, Xiangang Huang, Jianguo Zhang, Chen Ye, Yong Zhang, Jianfei Hu, Kunlin Zhang, Xin Xu, Lijuan Cong, Hong Lu, Xide Ren, Xiaoyu Ren, Jun He, Lin Tao, Douglas A Passey, Jian Wang, Huanming Yang, Jun Yu, Songgang Li.   

Abstract

We describe a sequence assembler, RePS (repeat-masked Phrap with scaffolding), that explicitly identifies exact 20mer repeats from the shotgun data and removes them prior to the assembly. The established software is used to compute meaningful error probabilities for each base. Clone-end-pairing information is used to construct scaffolds that order and orient the contigs. We show with real data for human and rice that reasonable assemblies are possible even at coverages of only 4x to 6x, despite having up to 42.2% in exact repeats.

Entities:  

Mesh：

Year:  2002        PMID： 11997349      PMCID： PMC186573          DOI： 10.1101/gr.165102

Source DB:  PubMed          Journal:  Genome Res        ISSN： 1088-9051            Impact factor:   9.043


  24 in total

1.  The Staden package, 1998.

Authors:  R Staden; K F Beal; J K Bonfield
Journal:  Methods Mol Biol       Date:  2000

2.  Initial sequencing and analysis of the human genome.

Authors:  E S Lander; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; Y Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; J Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; A Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; M C Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; P Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; J B Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; S L Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; A P Abola; M J Proctor; R M Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; R Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; E E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; H Hermjakob; K Hokamp; W Jang; L S Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W J Kent; P Kitts; E V Koonin; I Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; J V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; E Stupka; J Szustakowki; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Journal:  Nature       Date:  2001-02-15       Impact factor: 49.962

3.  Design of a compartmentalized shotgun assembler for the human genome.

Authors:  D H Huson; K Reinert; S A Kravitz; K A Remington; A L Delcher; I M Dew; M Flanigan; A L Halpern; Z Lai; C M Mobarry; G G Sutton; E W Myers
Journal:  Bioinformatics       Date:  2001       Impact factor: 6.937

4.  An Eulerian path approach to DNA fragment assembly.

Authors:  P A Pevzner; H Tang; M S Waterman
Journal:  Proc Natl Acad Sci U S A       Date:  2001-08-14       Impact factor: 11.205

5.  Assembly of the working draft of the human genome with GigAssembler.

Authors:  W J Kent; D Haussler
Journal:  Genome Res       Date:  2001-09       Impact factor: 9.043

6.  A whole-genome assembly of Drosophila.

Authors:  E W Myers; G G Sutton; A L Delcher; I M Dew; D P Fasulo; M J Flanigan; S A Kravitz; C M Mobarry; K H Reinert; K A Remington; E L Anson; R A Bolanos; H H Chou; C M Jordan; A L Halpern; S Lonardi; E M Beasley; R C Brandon; L Chen; P J Dunn; Z Lai; Y Liang; D R Nusskern; M Zhan; Q Zhang; X Zheng; G M Rubin; M D Adams; J C Venter
Journal:  Science       Date:  2000-03-24       Impact factor: 47.728

7.  Rice transposable elements: a survey of 73,000 sequence-tagged-connectors.

Authors:  L Mao; T C Wood; Y Yu; M A Budiman; J Tomkins; S Woo; M Sasinowski; G Presting; D Frisch; S Goff; R A Dean; R A Wing
Journal:  Genome Res       Date:  2000-07       Impact factor: 9.043

8.  ARACHNE: a whole-genome shotgun assembler.

Authors:  Serafim Batzoglou; David B Jaffe; Ken Stanley; Jonathan Butler; Sante Gnerre; Evan Mauceli; Bonnie Berger; Jill P Mesirov; Eric S Lander
Journal:  Genome Res       Date:  2002-01       Impact factor: 9.043

9.  Survey of transposable elements from rice genomic sequences.

Authors:  K Turcotte; S Srinivasan; T Bureau
Journal:  Plant J       Date:  2001-01       Impact factor: 6.417

10.  The sequence of the human genome.

Authors:  J C Venter; M D Adams; E W Myers; P W Li; R J Mural; G G Sutton; H O Smith; M Yandell; C A Evans; R A Holt; J D Gocayne; P Amanatides; R M Ballew; D H Huson; J R Wortman; Q Zhang; C D Kodira; X H Zheng; L Chen; M Skupski; G Subramanian; P D Thomas; J Zhang; G L Gabor Miklos; C Nelson; S Broder; A G Clark; J Nadeau; V A McKusick; N Zinder; A J Levine; R J Roberts; M Simon; C Slayman; M Hunkapiller; R Bolanos; A Delcher; I Dew; D Fasulo; M Flanigan; L Florea; A Halpern; S Hannenhalli; S Kravitz; S Levy; C Mobarry; K Reinert; K Remington; J Abu-Threideh; E Beasley; K Biddick; V Bonazzi; R Brandon; M Cargill; I Chandramouliswaran; R Charlab; K Chaturvedi; Z Deng; V Di Francesco; P Dunn; K Eilbeck; C Evangelista; A E Gabrielian; W Gan; W Ge; F Gong; Z Gu; P Guan; T J Heiman; M E Higgins; R R Ji; Z Ke; K A Ketchum; Z Lai; Y Lei; Z Li; J Li; Y Liang; X Lin; F Lu; G V Merkulov; N Milshina; H M Moore; A K Naik; V A Narayan; B Neelam; D Nusskern; D B Rusch; S Salzberg; W Shao; B Shue; J Sun; Z Wang; A Wang; X Wang; J Wang; M Wei; R Wides; C Xiao; C Yan; A Yao; J Ye; M Zhan; W Zhang; H Zhang; Q Zhao; L Zheng; F Zhong; W Zhong; S Zhu; S Zhao; D Gilbert; S Baumhueter; G Spier; C Carter; A Cravchik; T Woodage; F Ali; H An; A Awe; D Baldwin; H Baden; M Barnstead; I Barrow; K Beeson; D Busam; A Carver; A Center; M L Cheng; L Curry; S Danaher; L Davenport; R Desilets; S Dietz; K Dodson; L Doup; S Ferriera; N Garg; A Gluecksmann; B Hart; J Haynes; C Haynes; C Heiner; S Hladun; D Hostin; J Houck; T Howland; C Ibegwam; J Johnson; F Kalush; L Kline; S Koduru; A Love; F Mann; D May; S McCawley; T McIntosh; I McMullen; M Moy; L Moy; B Murphy; K Nelson; C Pfannkoch; E Pratts; V Puri; H Qureshi; M Reardon; R Rodriguez; Y H Rogers; D Romblad; B Ruhfel; R Scott; C Sitter; M Smallwood; E Stewart; R Strong; E Suh; R Thomas; N N Tint; S Tse; C Vech; G Wang; J Wetter; S Williams; M Williams; S Windsor; E Winn-Deen; K Wolfe; J Zaveri; K Zaveri; J F Abril; R Guigó; M J Campbell; K V Sjolander; B Karlak; A Kejariwal; H Mi; B Lazareva; T Hatton; A Narechania; K Diemer; A Muruganujan; N Guo; S Sato; V Bafna; S Istrail; R Lippert; R Schwartz; B Walenz; S Yooseph; D Allen; A Basu; J Baxendale; L Blick; M Caminha; J Carnes-Stine; P Caulk; Y H Chiang; M Coyne; C Dahlke; A Deslattes Mays; M Dombroski; M Donnelly; D Ely; S Esparham; C Fosler; H Gire; S Glanowski; K Glasser; A Glodek; M Gorokhov; K Graham; B Gropman; M Harris; J Heil; S Henderson; J Hoover; D Jennings; C Jordan; J Jordan; J Kasha; L Kagan; C Kraft; A Levitsky; M Lewis; X Liu; J Lopez; D Ma; W Majoros; J McDaniel; S Murphy; M Newman; T Nguyen; N Nguyen; M Nodell; S Pan; J Peck; M Peterson; W Rowe; R Sanders; J Scott; M Simpson; T Smith; A Sprague; T Stockwell; R Turner; E Venter; M Wang; M Wen; D Wu; M Wu; A Xia; A Zandieh; X Zhu
Journal:  Science       Date:  2001-02-16       Impact factor: 47.728
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  23 in total

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Authors:  Xiaoqiu Huang; Jianmin Wang; Srinivas Aluru; Shiaw-Pyng Yang; LaDeana Hillier
Journal:  Genome Res       Date:  2003-09       Impact factor: 9.043

2.  Estimating the repeat structure and length of DNA sequences using L-tuples.

Authors:  Xiaoman Li; Michael S Waterman
Journal:  Genome Res       Date:  2003-08       Impact factor: 9.043

3.  De novo repeat classification and fragment assembly.

Authors:  Pavel A Pevzner; Paul A Pevzner; Haixu Tang; Glenn Tesler
Journal:  Genome Res       Date:  2004-09       Impact factor: 9.043

4.  Assembly of large genomes using second-generation sequencing.

Authors:  Michael C Schatz; Arthur L Delcher; Steven L Salzberg
Journal:  Genome Res       Date:  2010-05-27       Impact factor: 9.043

5.  A tandem duplication of manganese superoxide dismutase in Nosema bombycis and its evolutionary origins.

Authors:  Heng Xiang; Guoqing Pan; Charles R Vossbrinck; Ruizhi Zhang; Jinshan Xu; Tian Li; Zeyang Zhou; Cheng Lu; Zhonghuai Xiang
Journal:  J Mol Evol       Date:  2010-10-23       Impact factor: 2.395

6.  Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences.

Authors:  Zhen-Yu Gao; Shan-Cen Zhao; Wei-Ming He; Long-Biao Guo; You-Lin Peng; Jin-Jin Wang; Xiao-Sen Guo; Xue-Mei Zhang; Yu-Chun Rao; Chi Zhang; Guo-Jun Dong; Feng-Ya Zheng; Chang-Xin Lu; Jiang Hu; Qing Zhou; Hui-Juan Liu; Hai-Yang Wu; Jie Xu; Pei-Xiang Ni; Da-Li Zeng; Deng-Hui Liu; Peng Tian; Li-Hui Gong; Chen Ye; Guang-Heng Zhang; Jian Wang; Fu-Kuan Tian; Da-Wei Xue; Yi Liao; Li Zhu; Ming-Sheng Chen; Jia-Yang Li; Shi-Hua Cheng; Geng-Yun Zhang; Jun Wang; Qian Qian
Journal:  Proc Natl Acad Sci U S A       Date:  2013-08-12       Impact factor: 11.205

7.  De novo assembly of human genomes with massively parallel short read sequencing.

Authors:  Ruiqiang Li; Hongmei Zhu; Jue Ruan; Wubin Qian; Xiaodong Fang; Zhongbin Shi; Yingrui Li; Shengting Li; Gao Shan; Karsten Kristiansen; Songgang Li; Huanming Yang; Jian Wang; Jun Wang
Journal:  Genome Res       Date:  2009-12-17       Impact factor: 9.043

8.  The genome of the cucumber, Cucumis sativus L.

Authors:  Sanwen Huang; Ruiqiang Li; Zhonghua Zhang; Li Li; Xingfang Gu; Wei Fan; William J Lucas; Xiaowu Wang; Bingyan Xie; Peixiang Ni; Yuanyuan Ren; Hongmei Zhu; Jun Li; Kui Lin; Weiwei Jin; Zhangjun Fei; Guangcun Li; Jack Staub; Andrzej Kilian; Edwin A G van der Vossen; Yang Wu; Jie Guo; Jun He; Zhiqi Jia; Yi Ren; Geng Tian; Yao Lu; Jue Ruan; Wubin Qian; Mingwei Wang; Quanfei Huang; Bo Li; Zhaoling Xuan; Jianjun Cao; Zhigang Wu; Juanbin Zhang; Qingle Cai; Yinqi Bai; Bowen Zhao; Yonghua Han; Ying Li; Xuefeng Li; Shenhao Wang; Qiuxiang Shi; Shiqiang Liu; Won Kyong Cho; Jae-Yean Kim; Yong Xu; Katarzyna Heller-Uszynska; Han Miao; Zhouchao Cheng; Shengping Zhang; Jian Wu; Yuhong Yang; Houxiang Kang; Man Li; Huiqing Liang; Xiaoli Ren; Zhongbin Shi; Ming Wen; Min Jian; Hailong Yang; Guojie Zhang; Zhentao Yang; Rui Chen; Shifang Liu; Jianwen Li; Lijia Ma; Hui Liu; Yan Zhou; Jing Zhao; Xiaodong Fang; Guoqing Li; Lin Fang; Yingrui Li; Dongyuan Liu; Hongkun Zheng; Yong Zhang; Nan Qin; Zhuo Li; Guohua Yang; Shuang Yang; Lars Bolund; Karsten Kristiansen; Hancheng Zheng; Shaochuan Li; Xiuqing Zhang; Huanming Yang; Jian Wang; Rifei Sun; Baoxi Zhang; Shuzhi Jiang; Jun Wang; Yongchen Du; Songgang Li
Journal:  Nat Genet       Date:  2009-11-01       Impact factor: 38.330

9.  From bacterial genomics to metagenomics: concept, tools and recent advances.

Authors:  Pooja Sharma; Hansi Kumari; Mukesh Kumar; Mansi Verma; Kirti Kumari; Shweta Malhotra; Jitendra Khurana; Rup Lal
Journal:  Indian J Microbiol       Date:  2008-07-27       Impact factor: 2.461

10.  A helitron-like transposon superfamily from lepidoptera disrupts (GAAA)(n) microsatellites and is responsible for flanking sequence similarity within a microsatellite family.

Authors:  Brad S Coates; Douglas V Sumerford; Richard L Hellmich; Leslie C Lewis
Journal:  J Mol Evol       Date:  2010-03-09       Impact factor: 2.395
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