Bioinformatics Advance Access published online on December 8, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl629
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1 British Columbia Cancer Agency, Genome Sciences Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada
* To whom correspondence should be addressed.
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.
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
2 J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
René L. Warren, E-mail: rwarren{at}bcgsc.ca
Abstract
Associate Editor: Alex Bateman
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