Long-read, whole-genome shotgun sequence data for five model organisms

kristi Kim, Paul Peluso, Primo Babayan, Patricia Yeadon, Charles Yu, William Fisher, Chen-Shan Chin, Nicole Rapicavoli, David Rank, Joachim Li, David Catcheside, Susan Celniker, Adam Phillippy, Casey Bergman, Jane Landolin

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    71 Citations (Scopus)

    Abstract

    Single molecule, real-time (SMRT) sequencing from Pacific Biosciences is increasingly used in many areas of biological research including de novo genome assembly, structural-variant identification, haplotype phasing, mRNA isoform discovery, and base-modification analyses. High-quality, public datasets of SMRT sequences can spur development of analytic tools that can accommodate unique characteristics of SMRT data (long read lengths, lack of GC or amplification bias, and a random error profile leading to high consensus accuracy). In this paper, we describe eight high-coverage SMRT sequence datasets from five organisms (Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, Arabidopsis thaliana, and Drosophila melanogaster) that have been publicly released to the general scientific community (NCBI Sequence Read Archive ID SRP040522). Data were generated using two sequencing chemistries (P4C2 and P5C3) on the PacBio RS II instrument. The datasets reported here can be used without restriction by the research community to generate whole-genome assemblies, test new algorithms, investigate genome structure and evolution, and identify base modifications in some of the most widely-studied model systems in biological research.

    Original languageEnglish
    Article number140045
    JournalScientific Data - Nature
    Volume1
    DOIs
    Publication statusPublished - 2014

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  • Cite this

    Kim, K., Peluso, P., Babayan, P., Yeadon, P., Yu, C., Fisher, W., Chin, C-S., Rapicavoli, N., Rank, D., Li, J., Catcheside, D., Celniker, S., Phillippy, A., Bergman, C., & Landolin, J. (2014). Long-read, whole-genome shotgun sequence data for five model organisms. Scientific Data - Nature, 1, [140045]. https://doi.org/10.1038/sdata.2014.45