Hybrid error correction and de novo assembly of single-molecule sequencing reads

Journal Article

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. © 2012 Nature America, Inc. All rights reserved.

Full Text

Duke Authors

Cited Authors

  • Koren, S; Schatz, MC; Walenz, BP; Martin, J; Howard, JT; Ganapathy, G; Wang, Z; Rasko, DA; McCombie, WR; Jarvis, ED; Phillippy, AM

Published Date

  • 2012

Published In

Volume / Issue

  • 30 / 7

Start / End Page

  • 693 - 700

PubMed ID

  • 22750884

International Standard Serial Number (ISSN)

  • 1087-0156

Digital Object Identifier (DOI)

  • 10.1038/nbt.2280