Skip Navigation


Bioinformatics Advance Access originally published online on December 8, 2006
Bioinformatics 2007 23(4):500-501; doi:10.1093/bioinformatics/btl629
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrowOA All Versions of this Article:
23/4/500    most recent
btl629v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (3)
Google Scholar
Right arrow Articles by Warren, R. L.
Right arrow Articles by Holt, R. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Warren, R. L.
Right arrow Articles by Holt, R. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Assembling millions of short DNA sequences using SSAKE

René L. Warren *, Granger G. Sutton 1, Steven J. M. Jones and Robert A. Holt

British Columbia Cancer Agency, Genome Sciences Centre 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada
1 J. Craig Venter Institute, 9704 Medical Center Drive Rockville, MD 20850, USA

*To whom correspondence should be addressed.


  Abstract

Summary: Novel DNA sequencing technologies with the potential for up to three orders magnitude more sequence throughput than conventional Sanger sequencing are emerging. The instrument now available from Solexa Ltd, produces millions of short DNA sequences of 25 nt each. Due to ubiquitous repeats in large genomes and the inability of short sequences to uniquely and unambiguously characterize them, the short read length limits applicability for de novo sequencing. However, given the sequencing depth and the throughput of this instrument, stringent assembly of highly identical sequences can be achieved. We describe SSAKE, a tool for aggressively assembling millions of short nucleotide sequences by progressively searching through a prefix tree for the longest possible overlap between any two sequences. SSAKE is designed to help leverage the information from short sequence reads by stringently assembling them into contiguous sequences that can be used to characterize novel sequencing targets.

Availability: http://www.bcgsc.ca/bioinfo/software/ssake

Contact: rwarren{at}bcgsc.ca

Associate Editor: Alex Bateman

Received on October 6, 2006; revised on November 15, 2006; accepted on December 5, 2006

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


This article has been cited by other articles:


Home page
 Genome Res.Home page
D. Hernandez, P. Francois, L. Farinelli, M. Osteras, and J. Schrenzel
De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer
Genome Res., May 1, 2008; 18(5): 802 - 809.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
J. Butler, I. MacCallum, M. Kleber, I. A. Shlyakhter, M. K. Belmonte, E. S. Lander, C. Nusbaum, and D. B. Jaffe
ALLPATHS: De novo assembly of whole-genome shotgun microreads
Genome Res., May 1, 2008; 18(5): 810 - 820.
[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
 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
 BioinformaticsHome page
W. R. Jeck, J. A. Reinhardt, D. A. Baltrus, M. T. Hickenbotham, V. Magrini, E. R. Mardis, J. L. Dangl, and C. D. Jones
Extending assembly of short DNA sequences to handle error
Bioinformatics, November 1, 2007; 23(21): 2942 - 2944.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.