title: 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.
authors: National Biodefense Analysis and Countermeasures Center, Frederick, Maryland, USA. korens@nbacc.net
authors: Sergey
authors: S
authors: Koren
authors: Michael C
authors: MC
authors: Schatz
authors: Brian P
authors: BP
authors: Walenz
authors: Jeffrey
authors: J
authors: Martin
authors: Jason T
authors: JT
authors: Howard
authors: Ganeshkumar
authors: G
authors: Ganapathy
authors: Zhong
authors: Z
authors: Wang
authors: David A
authors: DA
authors: Rasko
authors: W Richard
authors: WR
authors: McCombie
authors: Erich D
authors: ED
authors: Jarvis
authors: Adam M Phillippy
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000235:genetics; D001435:Bacteriophages / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D012313:RNA / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics*; D003313:Zea mays / Q000235:genetics
chemical_list: D012313:RNA