Literature DB >> 21453517

A vertebrate case study of the quality of assemblies derived from next-generation sequences.

Liang Ye1, LaDeana W Hillier, Patrick Minx, Nay Thane, Devin P Locke, John C Martin, Lei Chen, Makedonka Mitreva, Jason R Miller, Kevin V Haub, David J Dooling, Elaine R Mardis, Richard K Wilson, George M Weinstock, Wesley C Warren.   

Abstract

The unparalleled efficiency of next-generation sequencing (NGS) has prompted widespread adoption, but significant problems remain in the use of NGS data for whole genome assembly. We explore the advantages and disadvantages of chicken genome assemblies generated using a variety of sequencing and assembly methodologies. NGS assemblies are equivalent in some ways to a Sanger-based assembly yet deficient in others. Nonetheless, these assemblies are sufficient for the identification of the majority of genes and can reveal novel sequences when compared to existing assembly references.

Entities:  

Mesh：

Substances：

Year:  2011        PMID： 21453517      PMCID： PMC3129681          DOI： 10.1186/gb-2011-12-3-r31

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


  21 in total

1.  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

2.  BLAT--the BLAST-like alignment tool.

Authors:  W James Kent
Journal:  Genome Res       Date:  2002-04       Impact factor: 9.043

3.  PCAP: a whole-genome assembly program.

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

4.  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

5.  Genome sequencing in microfabricated high-density picolitre reactors.

Authors:  Marcel Margulies; Michael Egholm; William E Altman; Said Attiya; Joel S Bader; Lisa A Bemben; Jan Berka; Michael S Braverman; Yi-Ju Chen; Zhoutao Chen; Scott B Dewell; Lei Du; Joseph M Fierro; Xavier V Gomes; Brian C Godwin; Wen He; Scott Helgesen; Chun Heen Ho; Chun He Ho; Gerard P Irzyk; Szilveszter C Jando; Maria L I Alenquer; Thomas P Jarvie; Kshama B Jirage; Jong-Bum Kim; James R Knight; Janna R Lanza; John H Leamon; Steven M Lefkowitz; Ming Lei; Jing Li; Kenton L Lohman; Hong Lu; Vinod B Makhijani; Keith E McDade; Michael P McKenna; Eugene W Myers; Elizabeth Nickerson; John R Nobile; Ramona Plant; Bernard P Puc; Michael T Ronan; George T Roth; Gary J Sarkis; Jan Fredrik Simons; John W Simpson; Maithreyan Srinivasan; Karrie R Tartaro; Alexander Tomasz; Kari A Vogt; Greg A Volkmer; Shally H Wang; Yong Wang; Michael P Weiner; Pengguang Yu; Richard F Begley; Jonathan M Rothberg
Journal:  Nature       Date:  2005-07-31       Impact factor: 49.962

6.  Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps.

Authors:  Isheng J Tsai; Thomas D Otto; Matthew Berriman
Journal:  Genome Biol       Date:  2010-04-13       Impact factor: 13.583

Review 7.  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

8.  Whole-genome sequence assembly for mammalian genomes: Arachne 2.

Authors:  David B Jaffe; Jonathan Butler; Sante Gnerre; Evan Mauceli; Kerstin Lindblad-Toh; Jill P Mesirov; Michael C Zody; Eric S Lander
Journal:  Genome Res       Date:  2003-01       Impact factor: 9.043

9.  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

10.  Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

Authors: 
Journal:  Nature       Date:  2004-12-09       Impact factor: 49.962
View more
  16 in total

1.  Graph accordance of next-generation sequence assemblies.

Authors:  Guohui Yao; Liang Ye; Hongyu Gao; Patrick Minx; Wesley C Warren; George M Weinstock
Journal:  Bioinformatics       Date:  2011-10-23       Impact factor: 6.937

Review 2.  A beginner's guide to eukaryotic genome annotation.

Authors:  Mark Yandell; Daniel Ence
Journal:  Nat Rev Genet       Date:  2012-04-18       Impact factor: 53.242

Review 3.  Repetitive DNA and next-generation sequencing: computational challenges and solutions.

Authors:  Todd J Treangen; Steven L Salzberg
Journal:  Nat Rev Genet       Date:  2011-11-29       Impact factor: 53.242

4.  Complex evolutionary trajectories of sex chromosomes across bird taxa.

Authors:  Qi Zhou; Jilin Zhang; Doris Bachtrog; Na An; Quanfei Huang; Erich D Jarvis; M Thomas P Gilbert; Guojie Zhang
Journal:  Science       Date:  2014-12-11       Impact factor: 47.728

5.  Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism.

Authors:  John Archer; Jan Weber; Kenneth Henry; Dane Winner; Richard Gibson; Lawrence Lee; Ellen Paxinos; Eric J Arts; David L Robertson; Larry Mimms; Miguel E Quiñones-Mateu
Journal:  PLoS One       Date:  2012-11-14       Impact factor: 3.240

6.  A duck RH panel and its potential for assisting NGS genome assembly.

Authors:  Man Rao; Mireille Morisson; Thomas Faraut; Suzanne Bardes; Katia Fève; Emmanuelle Labarthe; Valérie Fillon; Yinhua Huang; Ning Li; Alain Vignal
Journal:  BMC Genomics       Date:  2012-09-28       Impact factor: 3.969

7.  Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing.

Authors:  Sebastiaan van Heesch; Wigard P Kloosterman; Nico Lansu; Frans-Paul Ruzius; Elizabeth Levandowsky; Clarence C Lee; Shiguo Zhou; Steve Goldstein; David C Schwartz; Timothy T Harkins; Victor Guryev; Edwin Cuppen
Journal:  BMC Genomics       Date:  2013-04-16       Impact factor: 3.969

8.  ConDeTri--a content dependent read trimmer for Illumina data.

Authors:  Linnéa Smeds; Axel Künstner
Journal:  PLoS One       Date:  2011-10-19       Impact factor: 3.240

9.  Emergence and evolution of the glycoprotein hormone and neurotrophin gene families in vertebrates.

Authors:  Sandra Dos Santos; Sylvie Mazan; Byrappa Venkatesh; Joëlle Cohen-Tannoudji; Bruno Quérat
Journal:  BMC Evol Biol       Date:  2011-11-15       Impact factor: 3.260

10.  Finishing bacterial genome assemblies with Mix.

Authors:  Hayssam Soueidan; Florence Maurier; Alexis Groppi; Pascal Sirand-Pugnet; Florence Tardy; Christine Citti; Virginie Dupuy; Macha Nikolski
Journal:  BMC Bioinformatics       Date:  2013-10-15       Impact factor: 3.169
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.