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Bioinformatics Vol. 17 no. 90001 2001
Pages S132-S139
© 2001 Oxford University Press

Design of a compartmentalized shotgun assembler for the human genome

Daniel H. Huson , Knut Reinert , Saul A. Kravitz , Karin A. Remington , Art L. Delcher , Ian M. Dew , Mike Flanigan , Aaron L. Halpern , Zhongwu Lai , Clark M. Mobarry , Granger G. Sutton and Eugene W. Myers

Informatics Research, Celera Genomics, 45 West Gude Drive, Rockville, 20850, USA

Received on February 5, 2001 ; revised on March 30, 2001 ; accepted on March 30, 2001

Two different strategies for determining the human genome are currently being pursued: one is the "clone-by-clone" approach, employed by the publicly funded project, and the other is the "whole genome shotgun assembler" approach, favored by researchers at Celera Genomics. An interim strategy employed at Celera, called compartmentalized shotgun assembly, makes use of preliminary data produced by both approaches. In this paper we describe the design, implementation and operation of the "compartmentalized shotgun assembler".

Contact: Knut.Reinert{at}celera.com


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