Genome Research Econo tag

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Jaffe, D. B.
Right arrow Articles by Lander, E. S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Jaffe, D. B.
Right arrow Articles by Lander, E. S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?
Vol 13, Issue 1, 91-96, January 2003

METHODS

Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2

David B. Jaffe1,2, Jonathan Butler1, Sante Gnerre1, Evan Mauceli1, Kerstin Lindblad-Toh1, Jill P. Mesirov1, Michael C. Zody1 and Eric S. Lander1,3

1Whitehead Institute/MIT Center for Genome Research, Cambridge, Massachusetts 02141, USA; 3Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Three principal changes were simultaneously made and applied to the assembly of the mouse genome, during a six-month period of development: (1) Supercontigs (scaffolds) were iteratively broken and rejoined using several criteria, yielding a 64-fold increase in length (N50), and apparent elimination of all global misjoins; (2) gaps between contigs in supercontigs were filled (partially or completely) by insertion of reads, as suggested by pairing within the supercontig, increasing the N50 contig length by 50%; (3) memory usage was reduced fourfold. The outcome of this mouse assembly and its analysis are described in (Mouse Genome Sequencing Consortium 2002).

2 Corresponding author.

E-MAIL jaffe{at}genome.wi.mit.edu; FAX (617) 258-9108.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.828403.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 DNA ResHome page
S. Sato, Y. Nakamura, T. Kaneko, E. Asamizu, T. Kato, M. Nakao, S. Sasamoto, A. Watanabe, A. Ono, K. Kawashima, et al.
Genome Structure of the Legume, Lotus japonicus
DNA Res, May 28, 2008; (2008) dsn008v1.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
W. Brockman, P. Alvarez, S. Young, M. Garber, G. Giannoukos, W. L. Lee, C. Russ, E. S. Lander, C. Nusbaum, and D. B. Jaffe
Quality scores and SNP detection in sequencing-by-synthesis systems
Genome Res., May 1, 2008; 18(5): 763 - 770.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
G. Denisov, B. Walenz, A. L. Halpern, J. Miller, N. Axelrod, S. Levy, and G. Sutton
Consensus generation and variant detection by Celera Assembler
Bioinformatics, April 15, 2008; 24(8): 1035 - 1040.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
M. J. Chaisson and P. A. Pevzner
Short read fragment assembly of bacterial genomes
Genome Res., February 1, 2008; 18(2): 324 - 330.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. V. Zimin, D. R. Smith, G. Sutton, and J. A. Yorke
Assembly reconciliation
Bioinformatics, January 1, 2008; 24(1): 42 - 45.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
J. U. Pontius, J. C. Mullikin, D. R. Smith, Agencourt Sequencing Team, K. Lindblad-Toh, S. Gnerre, M. Clamp, J. Chang, R. Stephens, B. Neelam, et al.
Initial sequence and comparative analysis of the cat genome
Genome Res., November 1, 2007; 17(11): 1675 - 1689.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
J. C. Dohm, C. Lottaz, T. Borodina, and H. Himmelbauer
SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing
Genome Res., November 1, 2007; 17(11): 1697 - 1706.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
J. K. Hane, R. G.T. Lowe, P. S. Solomon, K.-C. Tan, C. L. Schoch, J. W. Spatafora, P. W. Crous, C. Kodira, B. W. Birren, J. E. Galagan, et al.
Dothideomycete Plant Interactions Illuminated by Genome Sequencing and EST Analysis of the Wheat Pathogen Stagonospora nodorum
PLANT CELL, November 1, 2007; 19(11): 3347 - 3368.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
I. Ebersberger, P. Galgoczy, S. Taudien, S. Taenzer, M. Platzer, and A. von Haeseler
Mapping Human Genetic Ancestry
Mol. Biol. Evol., October 1, 2007; 24(10): 2266 - 2276.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
J. H. Kim, M. S. Waterman, and L. M. Li
Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi
Genome Res., July 1, 2007; 17(7): 1101 - 1110.
[Abstract] [Full Text] [PDF]

Home page
 ScienceHome page
V. Nene, J. R. Wortman, D. Lawson, B. Haas, C. Kodira, Z. Tu, B. Loftus, Z. Xi, K. Megy, M. Grabherr, et al.
Genome Sequence of Aedes aegypti, a Major Arbovirus Vector
Science, June 22, 2007; 316(5832): 1718 - 1723.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
R. Bruggmann, A. K. Bharti, H. Gundlach, J. Lai, S. Young, A. C. Pontaroli, F. Wei, G. Haberer, G. Fuks, C. Du, et al.
Uneven chromosome contraction and expansion in the maize genome
Genome Res., October 1, 2006; 16(10): 1241 - 1251.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
R. L. Warren, D. Varabei, D. Platt, X. Huang, D. Messina, S.-P. Yang, J. W. Kronstad, M. Krzywinski, W. C. Warren, J. W. Wallis, et al.
Physical map-assisted whole-genome shotgun sequence assemblies.
Genome Res., June 1, 2006; 16(6): 768 - 775.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
X. Huang, S.-P. Yang, A. T. Chinwalla, L. W. Hillier, P. Minx, E. R. Mardis, and R. K. Wilson
Application of a superword array in genome assembly
Nucleic Acids Res., January 5, 2006; 34(1): 201 - 205.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. L. Salzberg and J. A. Yorke
Beware of mis-assembled genomes
Bioinformatics, December 15, 2005; 21(24): 4320 - 4321.
[Full Text] [PDF]

Home page
 Genome Res.Home page
J. E. Galagan, M. R. Henn, L.-J. Ma, C. A. Cuomo, and B. Birren
Genomics of the fungal kingdom: Insights into eukaryotic biology
Genome Res., December 1, 2005; 15(12): 1620 - 1631.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
G. Haberer, S. Young, A. K. Bharti, H. Gundlach, C. Raymond, G. Fuks, E. Butler, R. A. Wing, S. Rounsley, B. Birren, et al.
Structure and Architecture of the Maize Genome
Plant Physiology, December 1, 2005; 139(4): 1612 - 1624.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
P. H. Degnan, A. B. Lazarus, and J. J. Wernegreen
Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects
Genome Res., August 1, 2005; 15(8): 1023 - 1033.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
J. P. Vinson, D. B. Jaffe, K. O'Neill, E. K. Karlsson, N. Stange-Thomann, S. Anderson, J. P. Mesirov, N. Satoh, Y. Satou, C. Nusbaum, et al.
Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
Genome Res., August 1, 2005; 15(8): 1127 - 1135.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
K. Malde, E. Coward, and I. Jonassen
A graph based algorithm for generating EST consensus sequences
Bioinformatics, April 15, 2005; 21(8): 1371 - 1375.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
D. Bartels, S. Kespohl, S. Albaum, T. Druke, A. Goesmann, J. Herold, O. Kaiser, A. Puhler, F. Pfeiffer, G. Raddatz, et al.
BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison
Bioinformatics, April 1, 2005; 21(7): 853 - 859.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
J. D. Jaffe, N. Stange-Thomann, C. Smith, D. DeCaprio, S. Fisher, J. Butler, S. Calvo, T. Elkins, M. G. FitzGerald, N. Hafez, et al.
The Complete Genome and Proteome of Mycoplasma mobile
Genome Res., August 1, 2004; 14(8): 1447 - 1461.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
P. Havlak, R. Chen, K. J. Durbin, A. Egan, Y. Ren, X.-Z. Song, G. M. Weinstock, and R. A. Gibbs
The Atlas Genome Assembly System
Genome Res., April 1, 2004; 14(4): 721 - 732.
[Abstract] [Full Text] [PDF]

Home page
 Microbiol. Mol. Biol. Rev.Home page
K. A. Borkovich, L. A. Alex, O. Yarden, M. Freitag, G. E. Turner, N. D. Read, S. Seiler, D. Bell-Pedersen, J. Paietta, N. Plesofsky, et al.
Lessons from the Genome Sequence of Neurospora crassa: Tracing the Path from Genomic Blueprint to Multicellular Organism
Microbiol. Mol. Biol. Rev., March 1, 2004; 68(1): 1 - 108.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
M. Pop, D. S. Kosack, and S. L. Salzberg
Hierarchical Scaffolding With Bambus
Genome Res., January 1, 2004; 14(1): 149 - 159.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
X. Huang, J. Wang, S. Aluru, S.-P. Yang, and L. Hillier
PCAP: A Whole-Genome Assembly Program
Genome Res., September 1, 2003; 13(9): 2164 - 2170.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.