Long-read, whole-genome shotgun sequence data for five model organisms - PubMed (original) (raw)

doi: 10.1038/sdata.2014.45. eCollection 2014.

Paul Peluso 1, Primo Babayan 1, P Jane Yeadon 2, Charles Yu 3, William W Fisher 3, Chen-Shan Chin 1, Nicole A Rapicavoli 1, David R Rank 1, Joachim Li 4, David E A Catcheside 2, Susan E Celniker 3, Adam M Phillippy 5, Casey M Bergman 6, Jane M Landolin 1

Affiliations

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

Kristi E Kim et al. Sci Data. 2014.

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.

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Conflict of interest statement

The authors declare competing financial interests. K.E.K., P.P., P.B., C.-S.C., N.A.R., D.R.R., and J.M.L. are employees of Pacific Biosciences of California, Inc., a company commercializing DNA sequencing technologies.

Figures

Figure 1

Figure 1. Mapped Subread Concordance and Coverage.

The distribution of mapped subread concordances and mapped subread coverages are plotted for E. coli MG1655 P4C2 (a), S. cerevisiae 9464 P4C2 (b), and D. melanogaster ISO1 P5C3 (c). The coverage distribution is similar among all chromosomes in S. cerevisiae, whereas the coverage distribution is half in chrX (50X) compared to the autosomes (100X) in D. melanogaster. ChrU and chrUextra are assembled contigs that could not be placed to physical chromosomes, and have very low coverages in general.

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