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METHODS: ARACHNE: A Whole-Genome Shotgun Assembler
- Serafim Batzoglou,
- David B. Jaffe,
- Ken Stanley,
- Jonathan Butler,
- Sante Gnerre,
- Evan Mauceli,
- Bonnie Berger,
- Jill P. Mesirov,
- and Eric S. Lander
Genome Res. January 1, 2002 12: 177-189; doi:10.1101/gr.208902
...ARACHNE: A Whole-Genome Shotgun Assembler Serafim Batzoglou 1 , 2 , 3 , David B. Jaffe 2 , 3 , 4 , Ken Stanley 2 , Jonathan Butler 2 , Sante Gnerre 2 , Evan Mauceli 2 , Bonnie Berger 1 , 5 , Jill P. Mesirov...
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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...
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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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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
....B., Butler, J., Gnerre, S., Mauceli, E., Lindblad-Toh, K., Mesirov, J.P., Zody, M.C., and Lander, E.S. 2003 . Whole- sequence assembly for mammalian s: ARACHNE 2. Genome Res. 13 : 91 –96. ↵ Kececioglu, J.D. and Myers, E.W. 1995 . Combinatorial algorithms for DNA sequence assembly. Algorithmica 13 : 7 –51...
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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...
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Resource: ECHO: A reference-free short-read error correction algorithm
- Wei-Chun Kao,
- Andrew H. Chan,
- and Yun S. Song
Genome Res. July 2011 21: 1181-1192; Published in Advance April 11, 2011, doi:10.1101/gr.111351.110
...coverage depth and the position in the read. The improvement is most pronounced toward the end of the read, where previous methods become noticeably less effective. Using a whole-genome yeast data set, it is demonstrated here that ECHO is capable of coping with nonuniform coverage. Also, it is shown...
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LETTER: Noncoding Sequences Conserved in a Limited Number of Mammals in the SIM2 Interval are Frequently Functional
- Kelly A. Frazer,
- Heng Tao,
- Kazutoyo Osoegawa,
- Pieter J. de Jong,
- Xiyin Chen,
- Mark F. Doherty,
- and David R. Cox
Genome Res. March 2004 14: 367-372; Published in Advance February 12, 2004, doi:10.1101/gr.1961204
...chromosome 21 sequences with orthologous mouse chromosome 16 sequences generated by the BLASTZ program ( Schwartz et al. 2003 ) were downloaded from the Pennsylvania State University “Whole Genome Human/Mouse Homology” Web site at http://bio.cse.psu.edu//hummus/:data set number 3, corresponding...
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LETTER: Uneven chromosome contraction and expansion in the maize genome
- Rémy Bruggmann,
- Arvind K. Bharti,
- Heidrun Gundlach,
- Jinsheng Lai,
- Sarah Young,
- Ana C. Pontaroli,
- Fusheng Wei,
- Georg Haberer,
- Galina Fuks,
- Chunguang Du,
- Christina Raymond,
- Matt C. Estep,
- Renyi Liu,
- Jeffrey L. Bennetzen,
- Agnes P. Chan,
- Pablo D. Rabinowicz,
- John Quackenbush,
- W. Brad Barbazuk,
- Rod A. Wing,
- Bruce Birren,
- Chad Nusbaum,
- Steve Rounsley,
- Klaus F.X. Mayer,
- and Joachim Messing
Genome Res. October 2006 16: 1241-1251; Published in Advance August 10, 2006, doi:10.1101/gr.5338906
...a similar whole genome duplication event, has only one orthologous region (4.9 Mb) on the short arm of chromosome 3, and can be used as reference for the maize homoeologous regions. Alignment of the three regions allowed identification of syntenic blocks, and indicated that the maize regions have undergone...
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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...
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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
...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...

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