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Literature DB >> 21191376

Assemblies: the good, the bad, the ugly.

Ewan Birney¹.

Abstract

Mesh：

Year: 2011 PMID： 21191376 DOI： 10.1038/nmeth0111-59

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

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5 in total

1. Beware of mis-assembled genomes.

Authors: Steven L Salzberg; James A Yorke
Journal: Bioinformatics Date: 2005-12-15 Impact factor: 6.937

2. 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

Review 3. Assembly algorithms for next-generation sequencing data.

Authors: Jason R Miller; Sergey Koren; Granger Sutton
Journal: Genomics Date: 2010-03-06 Impact factor: 5.736

4. A map of human genome variation from population-scale sequencing.

Authors: Gonçalo R Abecasis; David Altshuler; Adam Auton; Lisa D Brooks; Richard M Durbin; Richard A Gibbs; Matt E Hurles; Gil A McVean
Journal: Nature Date: 2010-10-28 Impact factor: 49.962

5. 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

5 in total

16 in total

Review 1. Application of large-scale sequencing to marker discovery in plants.

Authors: Robert J Henry; Mark Edwards; Daniel L E Waters; S Gopala Krishnan; Peter Bundock; Timothy R Sexton; Ardashir K Masouleh; Catherine J Nock; Julie Pattemore
Journal: J Biosci Date: 2012-11 Impact factor: 1.826

2. The devil is in the details: Transposable element analysis of the Tasmanian devil genome.

Authors: Maria A Nilsson
Journal: Mob Genet Elements Date: 2015-12-04

3. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Authors: Keith R Bradnam; Joseph N Fass; Anton Alexandrov; Paul Baranay; Michael Bechner; Inanç Birol; Sébastien Boisvert; Jarrod A Chapman; Guillaume Chapuis; Rayan Chikhi; Hamidreza Chitsaz; Wen-Chi Chou; Jacques Corbeil; Cristian Del Fabbro; T Roderick Docking; Richard Durbin; Dent Earl; Scott Emrich; Pavel Fedotov; Nuno A Fonseca; Ganeshkumar Ganapathy; Richard A Gibbs; Sante Gnerre; Elénie Godzaridis; Steve Goldstein; Matthias Haimel; Giles Hall; David Haussler; Joseph B Hiatt; Isaac Y Ho; Jason Howard; Martin Hunt; Shaun D Jackman; David B Jaffe; Erich D Jarvis; Huaiyang Jiang; Sergey Kazakov; Paul J Kersey; Jacob O Kitzman; James R Knight; Sergey Koren; Tak-Wah Lam; Dominique Lavenier; François Laviolette; Yingrui Li; Zhenyu Li; Binghang Liu; Yue Liu; Ruibang Luo; Iain Maccallum; Matthew D Macmanes; Nicolas Maillet; Sergey Melnikov; Delphine Naquin; Zemin Ning; Thomas D Otto; Benedict Paten; Octávio S Paulo; Adam M Phillippy; Francisco Pina-Martins; Michael Place; Dariusz Przybylski; Xiang Qin; Carson Qu; Filipe J Ribeiro; Stephen Richards; Daniel S Rokhsar; J Graham Ruby; Simone Scalabrin; Michael C Schatz; David C Schwartz; Alexey Sergushichev; Ted Sharpe; Timothy I Shaw; Jay Shendure; Yujian Shi; Jared T Simpson; Henry Song; Fedor Tsarev; Francesco Vezzi; Riccardo Vicedomini; Bruno M Vieira; Jun Wang; Kim C Worley; Shuangye Yin; Siu-Ming Yiu; Jianying Yuan; Guojie Zhang; Hao Zhang; Shiguo Zhou; Ian F Korf
Journal: Gigascience Date: 2013-07-22 Impact factor: 6.524

4. Elucidation of insertion elements carried on plasmids and in vitro construction of shuttle vectors from the toxic cyanobacterium Planktothrix.

Authors: Guntram Christiansen; Alexander Goesmann; Rainer Kurmayer
Journal: Appl Environ Microbiol Date: 2014-06-06 Impact factor: 4.792

5. The genome of the pear (Pyrus bretschneideri Rehd.).

Authors: Jun Wu; Zhiwen Wang; Zebin Shi; Shu Zhang; Ray Ming; Shilin Zhu; M Awais Khan; Shutian Tao; Schuyler S Korban; Hao Wang; Nancy J Chen; Takeshi Nishio; Xun Xu; Lin Cong; Kaijie Qi; Xiaosan Huang; Yingtao Wang; Xiang Zhao; Juyou Wu; Cao Deng; Caiyun Gou; Weili Zhou; Hao Yin; Gaihua Qin; Yuhui Sha; Ye Tao; Hui Chen; Yanan Yang; Yue Song; Dongliang Zhan; Juan Wang; Leiting Li; Meisong Dai; Chao Gu; Yuezhi Wang; Daihu Shi; Xiaowei Wang; Huping Zhang; Liang Zeng; Danman Zheng; Chunlei Wang; Maoshan Chen; Guangbiao Wang; Lin Xie; Valpuri Sovero; Shoufeng Sha; Wenjiang Huang; Shujun Zhang; Mingyue Zhang; Jiangmei Sun; Linlin Xu; Yuan Li; Xing Liu; Qingsong Li; Jiahui Shen; Junyi Wang; Robert E Paull; Jeffrey L Bennetzen; Jun Wang; Shaoling Zhang
Journal: Genome Res Date: 2012-11-13 Impact factor: 9.043

6. Graphical contig analyzer for all sequencing platforms (G4ALL): a new stand-alone tool for finishing and draft generation of bacterial genomes.

Authors: Rommel Thiago Jucá Ramos; Adriana R Carneiro; Pablo H Caracciolo; Vasco Azevedo; Maria Paula C Schneider; Debmalya Barh; Artur Silva
Journal: Bioinformation Date: 2013-06-29

7. Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes).

Authors: Christophe Dessimoz; Stefan Zoller; Tereza Manousaki; Huan Qiu; Axel Meyer; Shigehiro Kuraku
Journal: Brief Bioinform Date: 2011-06-28 Impact factor: 11.622