Hybrid error correction and de novo assembly of single-molecule sequencing reads.
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.
Type
Journal articleSubject
AlgorithmsBacteria
Bacteriophages
Computational Biology
RNA
Sequence Analysis, RNA
Transcriptome
Zea mays
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https://hdl.handle.net/10161/9301Published Version (Please cite this version)
10.1038/nbt.2280Publication Info
Koren, Sergey; Schatz, Michael C; Walenz, Brian P; Martin, Jeffrey; Howard, Jason
T; Ganapathy, Ganeshkumar; ... Adam M Phillippy (2012). Hybrid error correction and de novo assembly of single-molecule sequencing reads.
Nat Biotechnol, 30(7). pp. 693-700. 10.1038/nbt.2280. Retrieved from https://hdl.handle.net/10161/9301.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Show full item recordScholars@Duke
Erich David Jarvis
Adjunct Professor in the Deptartment of Neurobiology
Dr. Jarvis' laboratory studies the neurobiology of vocal communication. Emphasis is
placed on the molecular pathways involved in the perception and production of learned
vocalizations. They use an integrative approach that combines behavioral, anatomical,
electrophysiological and molecular biological techniques. The main animal model used
is songbirds, one of the few vertebrate groups that evolved the ability to learn vocalizations.
The generality of the discoveries is tested in other vocal lear

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