Literature DB >> 11473002

Design of a compartmentalized shotgun assembler for the human genome.

D H Huson1, 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.   

Abstract

Two different strategies for determining the human genome are currently being pursued: one is the "clone-by-clone" approach, employed by the publicly funded project, and the other is the "whole genome shotgun assembler" approach, favored by researchers at Celera Genomics. An interim strategy employed at Celera, called compartmentalized shotgun assembly, makes use of preliminary data produced by both approaches. In this paper we describe the design, implementation and operation of the "compartmentalized shotgun assembler".

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Year:  2001        PMID: 11473002     DOI: 10.1093/bioinformatics/17.suppl_1.s132

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  26 in total

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

Authors:  Jun Wang; 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
Journal:  Genome Res       Date:  2002-05       Impact factor: 9.043

2.  The Atlas genome assembly system.

Authors:  Paul Havlak; Rui Chen; K James Durbin; Amy Egan; Yanru Ren; Xing-Zhi Song; George M Weinstock; Richard A Gibbs
Journal:  Genome Res       Date:  2004-04       Impact factor: 9.043

3.  Whole-genome sequences of Bacillus subtilis and close relatives.

Authors:  Ashlee M Earl; Mark Eppinger; W Florian Fricke; M J Rosovitz; David A Rasko; Sean Daugherty; Richard Losick; Roberto Kolter; Jacques Ravel
Journal:  J Bacteriol       Date:  2012-05       Impact factor: 3.490

4.  Genome signatures of Escherichia coli O157:H7 isolates from the bovine host reservoir.

Authors:  Mark Eppinger; Mark K Mammel; Joseph E Leclerc; Jacques Ravel; Thomas A Cebula
Journal:  Appl Environ Microbiol       Date:  2011-03-18       Impact factor: 4.792

5.  A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes.

Authors:  Susanne M D Goldberg; Justin Johnson; Dana Busam; Tamara Feldblyum; Steve Ferriera; Robert Friedman; Aaron Halpern; Hoda Khouri; Saul A Kravitz; Federico M Lauro; Kelvin Li; Yu-Hui Rogers; Robert Strausberg; Granger Sutton; Luke Tallon; Torsten Thomas; Eli Venter; Marvin Frazier; J Craig Venter
Journal:  Proc Natl Acad Sci U S A       Date:  2006-07-13       Impact factor: 11.205

Review 6.  Next-generation gap.

Authors:  John D McPherson
Journal:  Nat Methods       Date:  2009-11       Impact factor: 28.547

7.  Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella.

Authors:  Eric W Schmidt; James T Nelson; David A Rasko; Sebastian Sudek; Jonathan A Eisen; Margo G Haygood; Jacques Ravel
Journal:  Proc Natl Acad Sci U S A       Date:  2005-05-09       Impact factor: 11.205

8.  Genomic anatomy of Escherichia coli O157:H7 outbreaks.

Authors:  Mark Eppinger; Mark K Mammel; Joseph E Leclerc; Jacques Ravel; Thomas A Cebula
Journal:  Proc Natl Acad Sci U S A       Date:  2011-11-30       Impact factor: 11.205

9.  Whole-genome shotgun assembly and comparison of human genome assemblies.

Authors:  Sorin Istrail; Granger G Sutton; Liliana Florea; Aaron L Halpern; Clark M Mobarry; Ross Lippert; Brian Walenz; Hagit Shatkay; Ian Dew; Jason R Miller; Michael J Flanigan; Nathan J Edwards; Randall Bolanos; Daniel Fasulo; Bjarni V Halldorsson; Sridhar Hannenhalli; Russell Turner; Shibu Yooseph; Fu Lu; Deborah R Nusskern; Bixiong Chris Shue; Xiangqun Holly Zheng; Fei Zhong; Arthur L Delcher; Daniel H Huson; Saul A Kravitz; Laurent Mouchard; Knut Reinert; Karin A Remington; Andrew G Clark; Michael S Waterman; Evan E Eichler; Mark D Adams; Michael W Hunkapiller; Eugene W Myers; J Craig Venter
Journal:  Proc Natl Acad Sci U S A       Date:  2004-02-09       Impact factor: 11.205

10.  Assembly complexity of prokaryotic genomes using short reads.

Authors:  Carl Kingsford; Michael C Schatz; Mihai Pop
Journal:  BMC Bioinformatics       Date:  2010-01-12       Impact factor: 3.169

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