Abstract

Massively parallel sequencing instruments enable rapid and inexpensive DNA sequence data production. Because these instruments are new, their data require characterization with respect to accuracy and utility. To address this, we sequenced a Caernohabditis elegans N2 Bristol strain isolate using the Solexa Sequence Analyzer, and compared the reads to the reference genome to characterize the data and to evaluate coverage and representation. Massively parallel sequencing facilitates strain-to-reference comparison for genome-wide sequence variant discovery. Owing to the short-read-length sequences produced, we developed a revised approach to determine the regions of the genome to which short reads could be uniquely mapped. We then aligned Solexa reads from C. elegans strain CB4858 to the reference, and screened for single-nucleotide polymorphisms (SNPs) and small indels. This study demonstrates the utility of massively parallel short read sequencing for whole genome resequencing and for accurate discovery of genome-wide polymorphisms.

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Acknowledgements

We acknowledge National Human Genome Research Institute funding (HG003079-04 to R.K.W. and HG003698 to G.T.M.). We thank K. Hall and D. Bentley of Illumina, Inc. for generously producing the paired-end read data described in the manuscript, M. Wendl for careful reading of the manuscript and T. Bieri for submitting the CB4858 variants to Wormbase.

Author information

Author notes

    • LaDeana W Hillier
    •  & Gabor T Marth

    These authors contributed equally to this work.

Affiliations

  1. Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd., St. Louis, Missouri 63108, USA.

    • LaDeana W Hillier
    • , David Dooling
    • , Ginger Fewell
    • , Paul Fox
    • , Jarret I Glasscock
    • , Matthew Hickenbotham
    • , Vincent J Magrini
    • , Ryan J Richt
    • , Sacha N Sander
    • , Todd Wylie
    • , Tim Schedl
    • , Richard K Wilson
    •  & Elaine R Mardis
  2. Boston College, Department of Biology, 140 Commonwealth Ave., Chestnut Hill, Massachusetts 02467, USA.

    • Gabor T Marth
    • , Aaron R Quinlan
    • , Derek Barnett
    • , Weichun Huang
    • , Donald A Stewart
    • , Michael Stromberg
    •  & Eric F Tsung

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Contributions

L.W.H., N2 Bristol read, coverage, variant and gap analyses; G.T.M., CB4858 SNP discovery and N2 Bristol error profile analysis; A.R.Q., CB4858 SNP discovery and validation analysis; D.D., Solexa analysis pipeline; G.F., validation assay design and analysis, D.B., Solexa base quality value analysis, P.F., preparation of N2 Bristol and CB4858 DNA, J.I.G., N2 Bristol read analysis; M.H., Solexa libraries and sequencing, W.H., microrepeat analysis, V.J.M., Solexa libraries and sequencing, R.J.R., N2 Bristol analysis; S.N.S., validation assays; D.A.S., microrepeat masking of C. elegans; M.S., Mosaik adaptation; E.F.T., microrepeat finding; T.W., N2 Bristol analysis, T.S., C. elegans strain selection; R.K.W., project origination; E.R.M., project coordination and manuscript preparation.

Corresponding author

Correspondence to Elaine R Mardis.

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    Supplementary Text and Figures

    Supplementary Figures 1–4, Supplementary Data, Supplementary Methods, Supplementary Table 1

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DOI

https://doi.org/10.1038/nmeth.1179

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