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Resource: Assemblathon 1: A competitive assessment of de novo short read assembly methods
- 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,
- and Benedict Paten
Genome Res. December 2011 21: 2224-2241; Published in Advance September 16, 2011, doi:10.1101/gr.126599.111
...structures closely related to them) in tools such as phrap (http://www.phrap.org/), GigAssembler (Kent and Haussler 2000), Celera (Myers et al. 2000; Venter et al. 2001), ARACHNE (Batzoglou et al. 2002), and Phusion (Mullikin and Ning 2003), which were used for numerous highquality assemblies such as human...
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Method: Scaffolding a Caenorhabditis nematode genome with RNA-seq
- Ali Mortazavi,
- Erich M. Schwarz,
- Brian Williams,
- Lorian Schaeffer,
- Igor Antoshechkin,
- Barbara J. Wold,
- and Paul W. Sternberg
Genome Res. December 2010 20: 1740-1747; Published in Advance October 27, 2010, doi:10.1101/gr.111021.110
...the euchromatic sequence of the human .Nature 431: 931–945. Kent WJ. 2002. BLAT—the BLAST-like aligment tool. Genome Res 12: 656– 664. Kent WJ, Haussler D. 2001. Assembly of the working draft of the human with GigAssembler. Genome Res 11: 1541–1548. Kiontke K, Fitch DHA. 2005. The phylogenetic relationships...
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Methods: Locating Sequence on FPC Maps and Selecting a Minimal Tiling Path
- Friedrich W. Engler,
- James Hatfield,
- William Nelson,
- and Carol A. Soderlund
Genome Res. September 2003 13: 2152-2163; Published in Advance January 1, 2003, doi:10.1101/gr.1068603
..., but a program such as GigAssembler ( Kent and Haussler 2001 ) is written specifically for this application, and therefore, should be the program of choice for this task. Because there are many sequencing projects that have an FPC map, BESs, and draft sequence available, we have developed an algorithm called...
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INSIGHT/OUTLOOK: Assembling Puzzles from Preassembled Blocks
- Pavel A. Pevzner
Genome Res. September 1, 2001 11: 1461-1462; doi:10.1101/gr.206301
...to make the blue-eye principle work. After implementing GigAssembler and assembling the public working draft of the human , they proved that it is indeed the case ( International Human Genome Sequencing Consortium 2001 ). Although GigAssembler is based on a simple greedy principle, the implementation has...
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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
.... ↵ Jaffe D.B. , Butler J. , Gnerre S. , Mauceli E. , Lindblad-Toh K. , Mesirov J.P. , Zody M.C. , Lander E.S. ( 2003 ) Whole- sequence assembly for mammalian s: Arachne 2. Genome Res. 13 : 91 – 96 . ↵ Kent W.J. , Haussler D. ( 2001 ) Assembly of the working draft of the human with GigAssembler. Genome Res...
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RESOURCE: The Atlas Genome Assembly System
- Paul Havlak,
- Rui Chen,
- K. James Durbin,
- Amy Egan,
- Yanru Ren,
- Xing-Zhi Song,
- George M. Weinstock,
- and Richard A. Gibbs
Genome Res. April 2004 14: 721-732; doi:10.1101/gr.2264004
...with non-sequence-based methods. Use of BACs allows correction of artifacts due to repeats at each stage of the process. This is aided by ancillary data such as BAC fingerprint, other genomic maps, and syntenic relations with other genomes. Atlas was used to assemble a draft DNA sequence of the rat genome...
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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
...-purpose scaffolder, called Bambus, which affords users significant flexibility in controlling the scaffolding parameters. Bambus was used recently to scaffold the low-coverage draft dog genome data. Most significantly, Bambus enables the use of linking data other than that inferred from mate-pair information...
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RESOURCE: GALA, a Database for Genomic Sequence Alignments and Annotations
- Belinda Giardine,
- Laura Elnitski,
- Cathy Riemer,
- Izabela Makalowska,
- Scott Schwartz,
- Webb Miller,
- and Ross C. Hardison
Genome Res. April 1, 2003 13: 732-741; doi:10.1101/gr.603103
.... ↵ Kent W.J. , Haussler D. ( 2001 ) Assembly of the working draft of the human with GigAssembler. Genome Res. 11 : 1541 – 1548 . ↵ Kent W.J. , Sugnet C.W. , Furey T.S. , Roskin K.M. , Pringle T.H. , Zahler A.M. , Haussler D. ( 2002 ) The human browser at UCSC. Genome Res. 12 : 996 – 1006 . ↵ Kong A...
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LETTER: Identification of Candidate Genes Regulating HDL Cholesterol Using a Chromosomal Region Expression Array
- Laura A. Cox,
- Shifra Birnbaum,
- and John L. VandeBerg
Genome Res. November 1, 2002 12: 1693-1702; Published in Advance October 15, 2002, doi:10.1101/gr.333502
...– 664 . ↵ Kent W.J. , Haussler D. ( 2001 ) Assembly of the working draft of the human with GigAssembler. Genome Res. 11 : 1541 – 8 . ↵ Kent W.J. , Sugnet C.W. , Furey T.S. , Roskin K.M. , Pringle T.H. , Zahler A.M. , Haussler D. ( 2002 ) The human browser at UCSC. Genome Res. 12 : 996 – 1006 . ↵ Lander...
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LETTER: Selecting for Functional Alternative Splices in ESTs
- Zhengyan Kan,
- David States,
- and Warren Gish
Genome Res. December 1, 2002 12: 1837-1845; doi:10.1101/gr.764102
....J. ( 2001 ) Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res. 11 : 875 – 888 . ↵ Kent J.W. , Haussler D. ( 2001 ) Assembly of the working draft of the human with GigAssembler. Genome Res. 11 : 1541 – 1548 . ↵ Kochiwa H. , Suzuki R. , Washio T. , Saito R...

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