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. (July 2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology, 30 (7). pp. 693-700. ISSN 1087-0156
Abstract
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.
| Item Type: | Paper |
|---|---|
| Subjects: | Investigative techniques and equipment Investigative techniques and equipment > assays Investigative techniques and equipment > whole exome sequencing Investigative techniques and equipment > assays > whole exome sequencing |
| CSHL Authors: | |
| Communities: | CSHL Cancer Center Program > Cancer Genetics CSHL Cancer Center Shared Resources > DNA Sequencing Service CSHL labs > McCombie lab CSHL labs > Schatz lab |
| Depositing User: | Matt Covey |
| Date: | 1 July 2012 |
| Date Deposited: | 30 Jan 2013 19:59 |
| Last Modified: | 19 Jul 2021 20:43 |
| PMCID: | PMC3707490 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/26981 |
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