Searching journal content for articles similar to Batzoglou et al. 12 (1): 177.

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  1. METHODS: Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2
    • David B. Jaffe,
    • Jonathan Butler,
    • Sante Gnerre,
    • Evan Mauceli,
    • Kerstin Lindblad-Toh,
    • Jill P. Mesirov,
    • Michael C. Zody,
    • and Eric S. Lander
    Genome Res. January 1, 2003 13: 91-96; doi:10.1101/gr.828403
    ...Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2 David B. Jaffe 1 , 2 , Jonathan Butler 1 , Sante Gnerre 1 , Evan Mauceli 1 , Kerstin Lindblad-Toh 1 , Jill P. Mesirov 1 , Michael C. Zody 1 , and Eric...
  2. RESOURCE: ALLPATHS: De novo assembly of whole-genome shotgun microreads
    • Jonathan Butler,
    • Iain MacCallum,
    • Michael Kleber,
    • Ilya A. Shlyakhter,
    • Matthew K. Belmonte,
    • Eric S. Lander,
    • Chad Nusbaum,
    • and David B. Jaffe
    Genome Res. May 2008 18: 810-820; Published in Advance March 13, 2008, doi:10.1101/gr.7337908
    ...ALLPATHS: De novo assembly of whole-genome shotgun microreads Jonathan Butler 1 , Iain MacCallum 1 , Michael Kleber 1 , 6 , Ilya A. Shlyakhter 1 , Matthew K. Belmonte 1 , 2 , Eric S. Lander 1 , 3 , 4 , 5 , Chad...
  3. Methods: Physical map-assisted whole-genome shotgun sequence assemblies
    • René L. Warren,
    • Dmitry Varabei,
    • Darren Platt,
    • Xiaoqiu Huang,
    • David Messina,
    • Shiaw-Pyng Yang,
    • James W. Kronstad,
    • Martin Krzywinski,
    • Wesley C. Warren,
    • John W. Wallis,
    • LaDeana W. Hillier,
    • Asif T. Chinwalla,
    • Jacqueline E. Schein,
    • Asim S. Siddiqui,
    • Marco A. Marra,
    • Richard K. Wilson,
    • and Steven J.M. Jones
    Genome Res. June 2006 16: 768-775; doi:10.1101/gr.5090606
    ...Physical map-assisted whole-genome shotgun sequence assemblies Map-assisted WGAs René L. Warren 1 , 6 , Dmitry Varabei 1 , 6 , Darren Platt 4 , Xiaoqiu Huang 3 , David Messina 2 , Shiaw-Pyng Yang 2 , James W. Kronstad 5...
  4. METHODS: The Phusion Assembler
    • James C. Mullikin and
    • Zemin Ning
    Genome Res. January 1, 2003 13: 81-90; Published in Advance December 30, 2002, doi:10.1101/gr.731003
    ...the whole-genome shotgun (WGS) dataset collected by the Mouse Genome Sequencing Consortium, at ∼7.5× sequence coverage, producing a high-quality draft assembly 2.6 gigabases in size, of which 90% of these bases are in 479 scaffolds. For the mouse genome, which is a large and repeat-rich genome, the input...
  5. Methods: PCAP: A Whole-Genome Assembly Program
    • Xiaoqiu Huang,
    • Jianmin Wang,
    • Srinivas Aluru,
    • Shiaw-Pyng Yang,
    • and LaDeana Hillier
    Genome Res. September 2003 13: 2164-2170; doi:10.1101/gr.1390403
    ...PCAP: A Whole-Genome Assembly Program Xiaoqiu Huang 1 , 4 , Jianmin Wang 1 , Srinivas Aluru 2 , Shiaw-Pyng Yang 3 , and LaDeana Hillier 3 1 Department of Computer Science Iowa State University, Ames, Iowa 50011-1040, USA...
  6. LETTER: Strategies and Tools for Whole-Genome Alignments
    • Olivier Couronne,
    • Alexander Poliakov,
    • Nicolas Bray,
    • Tigran Ishkhanov,
    • Dmitriy Ryaboy,
    • Edward Rubin,
    • Lior Pachter,
    • and Inna Dubchak
    Genome Res. January 1, 2003 13: 73-80; doi:10.1101/gr.762503
    ...Strategies and Tools for Whole-Genome Alignments Olivier Couronne 1 , 3 , Alexander Poliakov 1 , Nicolas Bray 1 , Tigran Ishkhanov 1 , Dmitriy Ryaboy 1 , Edward Rubin 1 , Lior Pachter 2 , 3 , and Inna Dubchak 1...
  7. METHODS: RePS: A Sequence Assembler That Masks Exact Repeats Identified from the Shotgun Data
    • 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,
    • and Songgang Li
    Genome Res. May 1, 2002 12: 824-831; doi:10.1101/gr.165102
    ....S. ( 2002 ) ARACHNE: A whole- shotgun assembler. Genome Res. 12 : 177 – 189 . ↵ Bouck J. , Miller W. , Gorrell J.H. , Muzny D. , Gibbs R.A. ( 1998 ) Analysis of the quality and utility of random shotgun sequencing at low redundancies. Genome Res. 8 : 1074 – 1084 . ↵ Edwards A. , Caskey T. ( 1991 ) Closure...
  8. Methods: Hierarchical Scaffolding With Bambus
    • Mihai Pop,
    • Daniel S. Kosack,
    • and Steven L. Salzberg
    Genome Res. January 2004 14: 149-159; doi:10.1101/gr.1536204
    ...information. This ordering of contigs is an essential step when finishing and analyzing the data from a whole-genome shotgun project. Most recent assemblers include a scaffolding module; however, users have little control over the scaffolding algorithm or the information produced. We thus developed a general...
  9. Methods: Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
    • Jade P. Vinson,
    • David B. Jaffe,
    • Keith O'Neill,
    • Elinor K. Karlsson,
    • Nicole Stange-Thomann,
    • Scott Anderson,
    • Jill P. Mesirov,
    • Nori Satoh,
    • Yutaka Satou,
    • Chad Nusbaum,
    • Bruce Birren,
    • James E. Galagan,
    • and Eric S. Lander
    Genome Res. August 2005 15: 1127-1135; doi:10.1101/gr.3722605
    ...of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan Abstract Whole-genome assembly is now used routinely to obtain high-quality draft sequence for the genomes of species with low levels of polymorphism. However, genome assembly remains extremely challenging for highly...
  10. Methods: Fosmid-Based Physical Mapping of the Histoplasma capsulatum Genome
    • Vincent Magrini,
    • Wesley C. Warren,
    • John Wallis,
    • William E. Goldman,
    • Jian Xu,
    • Elaine R. Mardis,
    • and John D. McPherson
    Genome Res. August 2004 14: 1603-1609; doi:10.1101/gr.2361404
    ...and G186A-R Whole Genome Shotgun (WGS) PCAP and ARACHNE assemblies are available for BLASTIN searches. http://.wustl.edu/projects/hcapsulatum/index.php?fpc=1 ; An additional link where the Histoplasma capsulatum FPC database can be downloaded. http://www.sanger.ac.uk/Software/Image ; A link to IMAGE...
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