The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
Open accessAbstract
Advances in sequencing technology allow genomes to be sequenced at vastly decreased costs. However, the assembled data frequently are highly fragmented with many gaps. We present a practical approach that uses Illumina sequences to improve draft genome assemblies by aligning sequences against contig ends and performing local assemblies to produce gap-spanning contigs. The continuity of a draft genome can thus be substantially improved, often without the need to generate new data.
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Cites
Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
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 · cited 2×
“Local assemblies have also recently been implemented in SOAPdenovo to resolve repeats in a de novo assembly [4].”
BackgroundMethodMullikin, J. C., & Ning, Z. (2003) · Genome Research · doi:10.1101/gr.731003 · Cited by 222
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Engel, P., Martinson, V. G., & Moran, N. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1202970109 · Cited by 874
Sequence-specific error profile of Illumina sequencers
Nakamura, K., Oshima, T., Morimoto, T., Ikeda, S., Yoshikawa, H., Shiwa, Y., Ishikawa, S., Linak, M. C., Hirai, A., Takahashi, H., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr344 · Cited by 600
A beginner’s guide to eukaryotic genome annotation
Yandell, M., & Ence, D. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3174 · Cited by 588
Comparative genomics of the major parasitic worms
International Helminth Genomes Consortium (2019) · Nature Genetics · doi:10.1038/s41588-018-0262-1 · Cited by 560
Nagarajan, N., & Pop, M. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3367 · Cited by 474
Metadata
- Authors
- Tsai, I. J., Otto, T. D., & Berriman, M.
- Venue
- Genome Biology
- Published
- 2010-04-13
- Volume
- 11
- Issue
- 4
- Pages
- R41-R41
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2171467729
- Cited by
- 281
- References
- 3
- FWCI
- 9.33
- Type
- journal article
- Language
- en
- Open access
- gold
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- Tsai, I. J., Otto, T. D., & Berriman, M. (2010). Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biology. https://doi.org/10.1186/gb-2010-11-4-r41
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