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.