Robust haplotype reconstruction of eukaryotic read data with Hapler

2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011

Volumn , Issue , 2011, Pages 141-146

  O'Neil, Shawn T ^a   Emrich, Scott J ^a  

^a University of Notre Dame   (United States)

Author keywords

Coloring; Graph; Haplotype; SNP

Indexed keywords

DATA SETS; ERROR RATE; GRAPH; HAPLOTYPES; SAMPLE DATA; SNP; SOFTWARE TOOL;

MEDICAL COMPUTING;

POPULATION STATISTICS;

EID: 79953835276     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICCABS.2011.5729869     Document Type: Conference Paper

References (14)

1. A. G. Clark, "Inference of haplotypes from PCR-amplified samples of diploid populations," Molecular Biology Evolution, vol. 7, no. 2, pp. 111-122, 1990.
2. R. Salem, J. Wessel, and N. Schork, "A comprehensive literature review of haplotyping software and methods for use with unrelated individuals," Human Genomics, vol. 2, no. 1, pp. 39-66, 2005.
3. S. T. O'Neil, J. D. K. Dzurisin, R. Carmichael, N. F. Lobo, S. J. Emrich, and J. J. Hellmann, "Population level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon," BMC Genomics, vol. 11, no. 1, pp. 310+, 2010.
4. N. Eriksson, L. Pachter, Y. Mitsuya, S. Rhee, C. Wang, B. Gharizadeh, M. Ronaghi, R. Shafer, and N. Beerenwinkel, "Viral Population Estimation Using Pyrosequencing," PLoS Computational Biology, vol. 4, no. 5, pp. e1 000 074+, 2008.
5. O. Zagordi, R. K., M. D̃Aumer, and N. Beerenwinkel, "Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies," Nucleic Acids Research, vol. 38, no. 21, pp. 7400-7409, 2010.
6. M. Xie, J. Wang, J. Chen, J. Wu, and X. Liu, "Computational models and algorithms for the single individual haplotyping problem," Current Bioinformatics, vol. 5, no. 1, pp. 18-28, 2010.
7. V. Bafna, S. Istrail, G. Lancia, and R. Rizzi, "Polynomial and APX-hard cases of the individual haplotyping problem," Theoretical Computer Science, vol. 335, no. 1, pp. 109-125, 2005. (Pubitemid 40574420)
8. Z. Li, L. Wu, Y. Zhao, and X. Zhang, "A dynamic programming algorithm for the k-haplotyping problem." Acta Mathematicae Applicatae Sinica, vol. 22, no. 3, pp. 405-412, 2006.
9. D. He, A. Choi, K. Pipatsrisawat, A. Darwiche, and E. Eskin, "Optimal algorithms for haplotype assembly from wholegenome sequence data," Bioinformatics, vol. 26, no. 12, p. i183, 2010.
10. A. R. Quinlan, D. A. Stewart, M. P. Stromberg, and G. T. Marth, "Pyrobayes: an improved base caller for SNP discovery in pyrosequences," Nature Methods, vol. 5, no. 2, pp. 179-181, 2008. (Pubitemid 351181747)
11. J. Wall and J. Pritchard, "Haplotype blocks and linkage disequilibrium in the human genome," Nature Reviews Genetics, vol. 4, no. 8, pp. 587-597, 2003. (Pubitemid 36917501)
12. G. Nemhauser, L. Trotter Jr, and R. Nauss, "Set partitioning and chain decomposition," Management Science, vol. 20, no. 11, pp. 1413-1423, 1974.
13. H. Kuhn, "The Hungarian method for the assignment problem," Naval research logistics quarterly, vol. 2, no. 1-2, pp. 83-97, 1955.
14. E. V. Zakharov, N. F. Lobo, C. Nowak, and J. Hellmann, "Introgression as a likely cause of mtdna paraphyly in two allopatric skippers (lepidoptera: Hesperiidae)," Heredity, vol. 102, pp. 590-599, 2009.