The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Hybrid error correction and de novo assembly of single-molecule sequencing reads
Open accessAbstract
Single-molecule sequencing instruments can generate multikilobase sequences with the potential to greatly improve genome and transcriptome assembly. However, the error rates of single-molecule reads are high, which has limited their use thus far to resequencing bacteria. To address this limitation, we introduce a correction algorithm and assembly strategy that uses short, high-fidelity sequences to correct the error in single-molecule sequences. We demonstrate the utility of this approach on reads generated by a PacBio RS instrument from phage, prokaryotic and eukaryotic whole genomes, including the previously unsequenced genome of the parrot Melopsittacus undulatus, as well as for RNA-Seq reads of the corn (Zea mays) transcriptome. Our long-read correction achieves >99.9% base-call accuracy, leading to substantially better assemblies than current sequencing strategies: in the best example, the median contig size was quintupled relative to high-coverage, second-generation assemblies. Greater gains are predicted if read lengths continue to increase, including the prospect of single-contig bacterial chromosome assembly.
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“…the error mitigation strategy used in this study over the computationally intensive approach of correcting individual PacBio reads prior to assembly 62 or the use of PacBio’s recent Circular Consensus Sequencing also known as HiFi Sequencing (HiFi/CCS) 63,64 where reads are partially corrected…”
Method
Metadata
- Authors
- Koren, S., Schatz, M. C., Walenz, B. P., Martin, J., Howard, J. T., Ganapathy, G., Wang, Z., Rasko, D. A., McCombie, W. R., Jarvis, E. D., & Phillippy, A. M.
- Venue
- Nature Biotechnology
- Published
- 2012-07
- Volume
- 30
- Issue
- 7
- Pages
- 693-700
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2157888653
- Cited by
- 1,011
- References
- 9
- FWCI
- 32.06
- Type
- journal article
- Language
- en
- Open access
- green
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