The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Assembling millions of short DNA sequences using SSAKE
Open accessAbstract
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
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Environmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
Cited by
Sequencing technologies – the next generation
Metzker, M. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2626 · Cited by 7,066
Next-generation DNA sequencing
Shendure, J., & Ji, H. (2008) · Nature Biotechnology · doi:10.1038/nbt1486 · Cited by 4,509
De novo assembly of human genomes with massively parallel short read sequencing
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926
Scaffolding pre-assembled contigs using SSPACE.
Boetzer, M., Henkel, C. V., Jansen, H. J., Butler, D., & Pirovano, W. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btq683 · Cited by 2,337
Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma
Castellarin, M., Warren, R. L., Freeman, J. D., Dreolini, L., Krzywinski, M., Strauss, J., Barnes, R., Watson, P., Allen-Vercoe, E., Moore, R. A., et al. (2012) · Genome Research · doi:10.1101/gr.126516.111 · Cited by 2,043
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Metadata
- Authors
- Warren, R. L., Sutton, G. G., Jones, S. J. M., & Holt, R. A.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-12-08
- Volume
- 23
- Issue
- 4
- Pages
- 500-501
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2171475724
- Cited by
- 495
- References
- 1
- FWCI
- 10.31
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Warren, R. L., Sutton, G. G., Jones, S. J. M., & Holt, R. A. (2007). Assembling millions of short DNA sequences using SSAKE. Bioinformatics. https://doi.org/10.1093/bioinformatics/btl629
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