Improving phrap-based assembly of the rat using "reliable" overlaps

PLoS ONE

Volumn 3, Issue 3, 2008, Pages

  Roberts, Michael ^a   Zimin, Aleksey V ^a   Hayes, Wayne ^a,b   Hunt, Brian R ^a   Ustun, Cevat ^a,c   White, James R ^a   Havlak, Paul ^d,e   Yorke, James ^a  

^a Bldg 142   (United States)

^b Irvine   (United States)

^c CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^d BAYLOR COLLEGE OF MEDICINE   (United States)

^e NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ALGORITHM; ANALYTICAL ERROR; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; COMPUTER PROGRAM; GENE SEQUENCE; GENETIC CODE; GENOME ANALYSIS; NONHUMAN; RAT; RELIABILITY; SEQUENCE ANALYSIS; ANIMAL; GENETICS; GENOME; REPRODUCIBILITY;

RATTUS; RATTUS NORVEGICUS;

ANIMALS; CHROMOSOMES, ARTIFICIAL, BACTERIAL; GENOME; RATS; REPRODUCIBILITY OF RESULTS;

EID: 46649088769     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0001836     Document Type: Article

References (15)

1. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res. 8: 175-185.
2. Ewing B, Green P (1998) Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8: 186-194.
3. Sutton GG, White O, Adams MD, Kerlavage AR (1995) TIGR Assembler: A New Tool for Assembling Large Shotgun Sequencing Projects. Genome Sci. and Technology 1: 9-19.
4. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, et al. (2000) A Whole-Genome Assembly of Drosophila. Science 287: 2196-2204.
5. Havlak P, Chen R, Durbin KJ, Egan A, Ren Y, et al. (2004) The Atlas Genome Assembly System. Genome Res. 14: 721-732.
6. Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, et al. (2002) ARACHNE: A Whole Genome Shotgun Assembler. Genome Res. 12: 177-189.
7. Mullikin JC, Ning Z (2003) The Phusion Assembler. Genome Res. 13: 81-90.
8. Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, et al. (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297: 1301-1310.
9. Huang X, Wang J, Aluru S, Yang SP, Hillier L (2003) PCAP: a whole-genome assembly program. Genome Res. 13(9): 2164-70.
10. Green P (1996) Phrap documentation. http://www.phrap.org/phredphrap/ phrap.html.
11. Roberts M, Hunt BR, Yorke JA, Bolanos R, Delcher A (2003) A Preprocessor for Shotgun Assembly of Large Genomes. Journal of Computational Biology 11: 734-752.
12. Rat Genome Sequencing Project Consortium (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428: 493-521.
13. Salzberg SL, Yorke J (2005) Beware of mis-assembled genomes. Bioinformatics 21: 133-154.
14. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, et al. (2003) Human-Mouse Alignments with BLASTZ. Genome Research 13: 103-107.
15. Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O (1999) Alignment of whole genomes. Nucleic Acids Res. 27: 2369-2376.