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Published online before print August 16, 2001, 10.1101/gr.183201
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Vol. 11, Issue 9, 1541-1548, September 2001

METHODS
Assembly of the Working Draft of the Human Genome with GigAssembler

W. James Kent,1,3 and David Haussler2

1 Department of Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA; 2 Howard Hughes Medical Institute, Department of Computer Science, University of California at Santa Cruz, Santa Cruz, California 95064, USA

The data for the public working draft of the human genome contains roughly 400,000 initial sequence contigs in ~30,000 large insert clones. Many of these initial sequence contigs overlap. A program, GigAssembler, was built to merge them and to order and orient the resulting larger sequence contigs based on mRNA, paired plasmid ends, EST, BAC end pairs, and other information. This program produced the first publicly available assembly of the human genome, a working draft containing roughly 2.7 billion base pairs and covering an estimated 88% of the genome that has been used for several recent studies of the genome. Here we describe the algorithm used by GigAssembler.

3 Corresponding author.

11:1541-1548 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
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