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Extending assembly of short DNA sequences to handle error
Open accessAbstract
Inexpensive de novo genome sequencing, particularly in organisms with small genomes, is now possible using several new sequencing technologies. Some of these technologies such as that from Illumina's Solexa Sequencing, produce high genomic coverage by generating a very large number of small reads (∼30 bp). While prior work shows that partial assembly can be performed by k-mer extension in error-free reads, this algorithm is unsuccessful with the sequencing error rates found in practice. We present VCAKE (Verified Consensus Assembly by K-mer Extension), a modification of simple k-mer extension that overcomes error by using high depth coverage. Though it is a simple modification of a previous approach, we show significant improvements in assembly results on simulated and experimental datasets that include error. Availability: http://152.2.15.114/~labweb/VCAKE Contact: william.jeck@gmail.com
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Cited by
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
Stem cell transcriptome profiling via massive-scale mRNA sequencing
Cloonan, N., Forrest, A. R. R., Kolle, G., Gardiner, B. B. A., Faulkner, G. J., Brown, M. K., Taylor, D. F., Steptoe, A. L., Wani, S., Bethel, G., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1223 · Cited by 1,035
Kreuze, J. F., Perez, A., Untiveros, M., Quispe, D., Fuentes, S., Barker, I., & Simon, R. (2009) · Virology · doi:10.1016/j.virol.2009.03.024 · Cited by 600
Nagarajan, N., & Pop, M. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3367 · Cited by 474
Metadata
- Authors
- Jeck, W. R., Reinhardt, J. A., Baltrus, D. A., Hickenbotham, M. T., Magrini, V., Mardis, E. R., Dangl, J. L., & Jones, C. D.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-09-24
- Volume
- 23
- Issue
- 21
- Pages
- 2942-2944
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2159998739
- Cited by
- 269
- References
- 0
- FWCI
- 9.46
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Jeck, W. R., Reinhardt, J. A., Baltrus, D. A., Hickenbotham, M. T., Magrini, V., Mardis, E. R., Dangl, J. L., & Jones, C. D. (2007). Extending assembly of short DNA sequences to handle error. Bioinformatics. https://doi.org/10.1093/bioinformatics/btm451
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