Literature DB >> 22491283

Test driving genome assemblers.

Wei Fan, Ruiqiang Li.   

Abstract

Mesh：

Year:  2012        PMID： 22491283     DOI： 10.1038/nbt.2172

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  12 in total

1.  GAGE: A critical evaluation of genome assemblies and assembly algorithms.

Authors:  Steven L Salzberg; Adam M Phillippy; Aleksey Zimin; Daniela Puiu; Tanja Magoc; Sergey Koren; Todd J Treangen; Michael C Schatz; Arthur L Delcher; Michael Roberts; Guillaume Marçais; Mihai Pop; James A Yorke
Journal:  Genome Res       Date:  2012-01-06       Impact factor: 9.043

2.  High-quality draft assemblies of mammalian genomes from massively parallel sequence data.

Authors:  Sante Gnerre; Iain Maccallum; Dariusz Przybylski; Filipe J Ribeiro; Joshua N Burton; Bruce J Walker; Ted Sharpe; Giles Hall; Terrance P Shea; Sean Sykes; Aaron M Berlin; Daniel Aird; Maura Costello; Riza Daza; Louise Williams; Robert Nicol; Andreas Gnirke; Chad Nusbaum; Eric S Lander; David B Jaffe
Journal:  Proc Natl Acad Sci U S A       Date:  2010-12-27       Impact factor: 11.205

3.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Authors:  Daniel R Zerbino; Ewan Birney
Journal:  Genome Res       Date:  2008-03-18       Impact factor: 9.043

4.  Bambus 2: scaffolding metagenomes.

Authors:  Sergey Koren; Todd J Treangen; Mihai Pop
Journal:  Bioinformatics       Date:  2011-09-16       Impact factor: 6.937

5.  Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Authors:  Dent Earl; Keith Bradnam; John St John; Aaron Darling; Dawei Lin; Joseph Fass; Hung On Ken Yu; Vince Buffalo; Daniel R Zerbino; Mark Diekhans; Ngan Nguyen; Pramila Nuwantha Ariyaratne; Wing-Kin Sung; Zemin Ning; Matthias Haimel; Jared T Simpson; Nuno A Fonseca; İnanç Birol; T Roderick Docking; Isaac Y Ho; Daniel S Rokhsar; Rayan Chikhi; Dominique Lavenier; Guillaume Chapuis; Delphine Naquin; Nicolas Maillet; Michael C Schatz; David R Kelley; Adam M Phillippy; Sergey Koren; Shiaw-Pyng Yang; Wei Wu; Wen-Chi Chou; Anuj Srivastava; Timothy I Shaw; J Graham Ruby; Peter Skewes-Cox; Miguel Betegon; Michelle T Dimon; Victor Solovyev; Igor Seledtsov; Petr Kosarev; Denis Vorobyev; Ricardo Ramirez-Gonzalez; Richard Leggett; Dan MacLean; Fangfang Xia; Ruibang Luo; Zhenyu Li; Yinlong Xie; Binghang Liu; Sante Gnerre; Iain MacCallum; Dariusz Przybylski; Filipe J Ribeiro; Shuangye Yin; Ted Sharpe; Giles Hall; Paul J Kersey; Richard Durbin; Shaun D Jackman; Jarrod A Chapman; Xiaoqiu Huang; Joseph L DeRisi; Mario Caccamo; Yingrui Li; David B Jaffe; Richard E Green; David Haussler; Ian Korf; Benedict Paten
Journal:  Genome Res       Date:  2011-09-16       Impact factor: 9.043

6.  Efficient de novo assembly of large genomes using compressed data structures.

Authors:  Jared T Simpson; Richard Durbin
Journal:  Genome Res       Date:  2011-12-07       Impact factor: 9.043

7.  The sequence and de novo assembly of the giant panda genome.

Authors:  Ruiqiang Li; Wei Fan; Geng Tian; Hongmei Zhu; Lin He; Jing Cai; Quanfei Huang; Qingle Cai; Bo Li; Yinqi Bai; Zhihe Zhang; Yaping Zhang; Wen Wang; Jun Li; Fuwen Wei; Heng Li; Min Jian; Jianwen Li; Zhaolei Zhang; Rasmus Nielsen; Dawei Li; Wanjun Gu; Zhentao Yang; Zhaoling Xuan; Oliver A Ryder; Frederick Chi-Ching Leung; Yan Zhou; Jianjun Cao; Xiao Sun; Yonggui Fu; Xiaodong Fang; Xiaosen Guo; Bo Wang; Rong Hou; Fujun Shen; Bo Mu; Peixiang Ni; Runmao Lin; Wubin Qian; Guodong Wang; Chang Yu; Wenhui Nie; Jinhuan Wang; Zhigang Wu; Huiqing Liang; Jiumeng Min; Qi Wu; Shifeng Cheng; Jue Ruan; Mingwei Wang; Zhongbin Shi; Ming Wen; Binghang Liu; Xiaoli Ren; Huisong Zheng; Dong Dong; Kathleen Cook; Gao Shan; Hao Zhang; Carolin Kosiol; Xueying Xie; Zuhong Lu; Hancheng Zheng; Yingrui Li; Cynthia C Steiner; Tommy Tsan-Yuk Lam; Siyuan Lin; Qinghui Zhang; Guoqing Li; Jing Tian; Timing Gong; Hongde Liu; Dejin Zhang; Lin Fang; Chen Ye; Juanbin Zhang; Wenbo Hu; Anlong Xu; Yuanyuan Ren; Guojie Zhang; Michael W Bruford; Qibin Li; Lijia Ma; Yiran Guo; Na An; Yujie Hu; Yang Zheng; Yongyong Shi; Zhiqiang Li; Qing Liu; Yanling Chen; Jing Zhao; Ning Qu; Shancen Zhao; Feng Tian; Xiaoling Wang; Haiyin Wang; Lizhi Xu; Xiao Liu; Tomas Vinar; Yajun Wang; Tak-Wah Lam; Siu-Ming Yiu; Shiping Liu; Hemin Zhang; Desheng Li; Yan Huang; Xia Wang; Guohua Yang; Zhi Jiang; Junyi Wang; Nan Qin; Li Li; Jingxiang Li; Lars Bolund; Karsten Kristiansen; Gane Ka-Shu Wong; Maynard Olson; Xiuqing Zhang; Songgang Li; Huanming Yang; Jian Wang; Jun Wang
Journal:  Nature       Date:  2009-12-13       Impact factor: 49.962

8.  Limitations of next-generation genome sequence assembly.

Authors:  Can Alkan; Saba Sajjadian; Evan E Eichler
Journal:  Nat Methods       Date:  2010-11-21       Impact factor: 28.547

9.  De novo assembly and genotyping of variants using colored de Bruijn graphs.

Authors:  Zamin Iqbal; Mario Caccamo; Isaac Turner; Paul Flicek; Gil McVean
Journal:  Nat Genet       Date:  2012-01-08       Impact factor: 38.330

10.  Aggressive assembly of pyrosequencing reads with mates.

Authors:  Jason R Miller; Arthur L Delcher; Sergey Koren; Eli Venter; Brian P Walenz; Anushka Brownley; Justin Johnson; Kelvin Li; Clark Mobarry; Granger Sutton
Journal:  Bioinformatics       Date:  2008-10-24       Impact factor: 6.937
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  1 in total

1.  Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species.

Authors:  Kyunghee Kim; Sang-Choon Lee; Junki Lee; Yeisoo Yu; Kiwoung Yang; Beom-Soon Choi; Hee-Jong Koh; Nomar Espinosa Waminal; Hong-Il Choi; Nam-Hoon Kim; Woojong Jang; Hyun-Seung Park; Jonghoon Lee; Hyun Oh Lee; Ho Jun Joh; Hyeon Ju Lee; Jee Young Park; Sampath Perumal; Murukarthick Jayakodi; Yun Sun Lee; Backki Kim; Dario Copetti; Soonok Kim; Sunggil Kim; Ki-Byung Lim; Young-Dong Kim; Jungho Lee; Kwang-Su Cho; Beom-Seok Park; Rod A Wing; Tae-Jin Yang
Journal:  Sci Rep       Date:  2015-10-28       Impact factor: 4.379
  1 in total

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