Assembling millions of short DNA sequences using SSAKE

被引：292

作者：

Warren, Rene L.

Sutton, Granger G.

Jones, Steven J. M.

Holt, Robert A.

机构：

[1] British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 1L3, Canada

[2] J Craig Venter Inst, Rockville, MD 20850 USA

来源：

BIOINFORMATICS | 2007年 / 23卷 / 04期

关键词：

D O I：

10.1093/bioinformatics/btl629

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：500 / 501

页数：2

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