The greedy path-merging algorithm for contig scaffolding

Journal of the ACM

Volumn 49, Issue 5, 2002, Pages 603-615

  Huson, Daniel H ^a   Reinert, Knut ^b   Myers, Eugene W ^c  

^a UNIVERSITY OF TÜBINGEN   (Germany)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Genome assembly

Indexed keywords

COMPARTMENTALIZED ASSEMBLY; CONTIG SCAFFOLDING; GENOME ASSEMBLY; GREEDY PATH-MERGING ALGORITHMS;

ALGORITHMS; CHROMOSOMES; DNA; DNA SEQUENCES; GENES; PROBLEM SOLVING; SAMPLING; STATISTICAL METHODS; VECTORS;

HUMAN ENGINEERING;

EID: 1242281253     PISSN: 00045411     EISSN: None     Source Type: Journal    
DOI: 10.1145/585265.585267     Document Type: Article

References (14)

1. BENSON, D. A., KARSCH-MIZRACHI, I., LIPMAN, D. J., OSTELL, J., RAPP, B. A., AND WHEELER, D. L. 2000. Genbank. Nuc. Acids Res. 28, 1, 15-8.
2. BEVINGTON, P. R. 1969. Data Reduction and Error Analysis for the Physical Sciences. McGraw-Hill, Inc., New York.
3. GAREY, M. R., AND JOHNSON, D. S. 1979. Computers and Intractability, A Guide to the Theory of NP-completeness. Bell Telephone Laboratories, Inc.
4. GREEN, P. 1994. Documentation for Phrap. http://bozeman.mbt.washington. edu/phrap.docs/phrap.html.
5. HUSON, D. H., REINERT, K., KRAVITZ, S. A., REMINGTON, K. A., DELCHER, A. L., DEW, I. M., FLANIGAN, M., HALPERN, A. L., LAI, Z., MOBARRY, C. M., SUTTON, G. G., AND MYERS, E. W. 2001. Design of a compartmentalized shotgun assembler for the human genome. Bioinformatics (Proceedings of ISMB 2001) 17, 132-139.
6. HUSON, D. H., REINERT, K., AND MYERS, E. W. 2001b. The greedy path-merging algorithm for sequence assembly. In Proceedings of the 5th Annual International Conference on Computational Molecular Biology (RECOMB-01), pp. 157-163.
7. INTERNATIONAL HUMAN GENOME SEQUENCING CONSORTIUM. 2001. Initial sequencing and analysis of the human genome. Nature 409, 6822, 860-921.
8. LANDER, E. S., AND WATERMAN, M. S. 1988. Genomic mapping by fingerprinting random clones: A mathematical analysis. Genomics 2, 231-239.
9. MYERS, E. W., SUTTON, G. G., DELCHER, A. L., DEW, I. M., FASULO, D. P., FLANIGAN, M. J., KRAVITZ, S. A., MOBARRY, C. M., REINERT, K. H. J., REMINGTON, K. A., ANSON, E. L., BOLANOS, R. A., CHOU, H.-H., JORDAN, C. M., HALPERN, A. L., LONARDI, S., BEASLEY, E. M., BRANDON, R. C., CHEN, L., DUNN, P. J., LAI, Z., LIANG, Y., NUSSKERN, D. R., ZHAN, M., ZHANG, Q., ZHENG, X., RUBIN, G. M., ADAMS, M. D., AND VENTER, J. C. 2000. A whole-genome assembly of Drosophila. Science 287, 2196-2204.
10. SANGER, F., COULSON, A. R., HONG, G. F., HILL, D. F., AND PETERSEN, G. B. 1992. Nucleotide sequence of bacteriophage λ DNA. J. Mol. Bio. 162, 4, 729-773.
11. SANGER, F., NICKLEN, S., AND COULSON, A. R. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Nat. Mad. Sci. 74, 12, 5463-5467.
12. U. S. DEPARTMENT OF ENERGY, OFFICE OF ENERGY RESEARCH, AND OFFICE OF BIOLOGICAL AND ENVIRONMENTAL RESEARCH. 1997. Human genome program report. http://www. ornl.gov/hgmis/publicat/97pr/.
13. VENTER, J. C., ADAMS, M. D., MYERS, E. W., ET AL. 2001. The sequence of the human genome. Science 291, 1145-1434.
14. WEBBER, J. L., AND MYERS, E. W. 1997. Human whole-genome shotgun sequencing. Gen. Res. 7, 5, 401-409.