Journal Article

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

Koren, Sergey, Schatz, Michael C, Martin, Jeffrey, Phillippy, Adam M, Rasko, David A, Howard, Jason T, Wang, Zhong, Walenz, Brian P, Jarvis, Erich D, Ganapathy, Ganeshkumar, McCombie, W Richard

2012

Overview

Single-molecule sequencing technologies can produce multikilobase-long reads, which are more useful than short reads for assembling genomes and transcriptomes, but their error rates are too high. Koren et al . correct long reads from a PacBio instrument using high-fidelity, short reads from complementary technologies, facilitating assembly of previously intractable sequences. 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.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 631/114 / 631/61/514/2254 / Agriculture / Algorithms / Bacteria / Bacteria - genetics / Bacteriophages - genetics / Bioinformatics / Biological and medical sciences / Biomedical and Life Sciences / Biomedical Engineering/Biotechnology / Biomedicine / Biotechnology / Chromosomes / Computational Biology - methods / Corn / Diverse techniques / DNA sequencing / Fundamental and applied biological sciences. Psychology / Genetic algorithms / Life Sciences / Melopsittacus undulatus / Molecular and cellular biology / Molecular biology / Nucleotide sequencing / Physiological aspects / RNA / RNA - genetics / Sequence Analysis, RNA - methods / Transcriptome - genetics / Zea mays / Zea mays - genetics