The greedy path-merging algorithm for sequence assembly

Authors:
Daniel H. Huson;Knut Reinert;Eugene Myers
Affiliations:
Informatics Research, Celera Genomics Corp., 45 W Gude Drive, Rockville, MD;Informatics Research, Celera Genomics Corp., 45 W Gude Drive, Rockville, MD;Informatics Research, Celera Genomics Corp., 45 W Gude Drive, Rockville, MD
Venue:
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Year:
2001

Citing 1
Cited 3

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The greedy path-merging algorithm for contig scaffolding

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Genome Sequence Assembly: Algorithms and Issues

Computer

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Abstract

Two different approaches to determining the human genome are currently being pursued: one is the “clone-by-clone” approach, employed by the publicly-funded. Human Genome Project, and the other is the “whole genome shotgun” approach, favored by researchers at Celera Genomics. An interim strategy employed at Celera, called hierarchical assembly, makes use of preliminary data produced by both approaches. This paper introduces the Bactig Ordering Problem, which is a key problem that arises in this context, and presents an efficient heuristic called the greedy path-merginq algorithm that performs well on real data.