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Article
Nature Methods - 5, 183 - 188 (2008)
Published online: 20 January 2008; | doi:10.1038/nmeth.1179

Whole-genome sequencing and variant discovery in C. elegans

LaDeana W Hillier1, 3, Gabor T Marth2, 3, Aaron R Quinlan2, David Dooling1, Ginger Fewell1, Derek Barnett2, Paul Fox1, Jarret I Glasscock1, Matthew Hickenbotham1, Weichun Huang2, Vincent J Magrini1, Ryan J Richt1, Sacha N Sander1, Donald A Stewart2, Michael Stromberg2, Eric F Tsung2, Todd Wylie1, Tim Schedl1, Richard K Wilson1 & Elaine R Mardis1

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

2  Boston College, Department of Biology, 140 Commonwealth Ave., Chestnut Hill, Massachusetts 02467, USA.

3  These authors contributed equally to this work.

Correspondence should be addressed to Elaine R Mardis emardis@watson.wustl.edu

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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Nature Methods
ISSN: 1548-7091
EISSN: 1548-7105
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