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Bioinformatics Advance Access published online on December 8, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl629
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© 2006 The Author(s)
Received October 6, 2006
Revised November 15, 2006
Accepted December 5, 2006

Applications note

Assembling millions of short DNA sequences using SSAKE

René L. Warren 1 *, Granger G. Sutton 2, Steven J. M. Jones 1, and Robert A. Holt 1

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

* To whom correspondence should be addressed.
René L. Warren, E-mail: rwarren{at}bcgsc.ca


  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 nucleotides 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.

Associate Editor: Alex Bateman
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