Hybrid error correction and de novo assembly of single-molecule sequencing reads.
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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.
Sequence Analysis, RNA
Published Version (Please cite this version)10.1038/nbt.2280
Publication InfoKoren, 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.
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Adjunct Professor in the Dept. 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