Assembling millions of short DNA sequences using SSAKE

Abstract

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: Contact: rwarren@bcgsc.ca

Keywords

DNA sequencingSanger sequencingComputational biologyHybrid genome assemblyBiologySequence assemblyGenomeSoftwareSequence (biology)k-merLeverage (statistics)Deep sequencingGeneticsDNAComputer scienceReference genomeGeneTranscriptomeArtificial intelligence

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Publication Info

Year: 2006
Type: article
Volume: 23
Issue: 4
Pages: 500-501
Citations: 500
Access: Closed

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APA Style

                            
                                
                                    Robin M. Warren, 
                                
                                    Granger G. Sutton, 
                                
                                    Steven J.M. Jones
                                
                                et al.
                            
                            (2006). 
                            Assembling millions of short DNA sequences using SSAKE. 
                            Bioinformatics
                            , 23
                            (4)
                            , 500-501.
                            https://doi.org/10.1093/bioinformatics/btl629
                        

Identifiers

DOI: 10.1093/bioinformatics/btl629