Quality score compression improves genotyping accuracy

Nature Biotechnology

Volumn 33, Issue 3, 2015, Pages 240-243

  Yu, Y William ^a,b   Yorukoglu, Deniz ^a   Peng, Jian ^a,b   Berger, Bonnie ^a,b  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SILICON DIOXIDE;

ACCURACY; COMPRESSION; GENE IDENTIFICATION; GENETIC VARIABILITY; GENOTYPE; LETTER; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL; RECEIVER OPERATING CHARACTERISTIC; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; ALGORITHM; GENOTYPING TECHNIQUE; HIGH THROUGHPUT SEQUENCING; HUMAN; INFORMATION PROCESSING; STANDARDS;

ALGORITHMS; DATA COMPRESSION; GENOTYPING TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; ROC CURVE;

EID: 84924360515     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.3170     Document Type: Letter

References (24)

1. Berger, B., Peng, J. & Singh, M. Nat. Rev. Genet. 14, 333-346 (2013).
2. Kahn, S.D. Science 331, 728-729 (2011).
3. The 1000 Genomes Project Consortium. Nature 491, 56-65 (2012).
4. Veeramah, K.R. & Hammer, M.F. Nat. Rev. Genet. 15, 149-162 (2014).
5. Shapiro, E., Biezuner, T. & Linnarsson, L. Nat. Rev. Genet. 14, 618-630 (2013).
6. Bonfield, J.K. & Mahoney, M.V. PLoS ONE 8, e59190 (2013).
7. Apostolico, A. & Lonardi, S. in Proceedings of the IEEE Data Compression Conference 2000 (DCC'00) 143-152 (IEEE Computer Society, 2000).
8. Kozanitis, C., Saunders, C., Kruglyak, S., Bafna, V. & Varghese, G. J. Comput. Biol. 18, 401-413 (2011).
9. Jones, D.C., Ruzzo, W.L., Peng, X. & Katze, M.G. Nucleic Acids Res. 40, e171 (2012).
10. Fritz, M.H.Y., Leinonen, R., Cochrane, G. & Birney, E. Genome Res. 21, 734-740 (2011).
11. Deorowicz, S. & Grabowski, S. Bioinformatics 27, 860-862 (2011).
12. Loh, P.R., Baym, M. & Berger, B. Nat. Biotechnol. 30, 627-630 (2012).
13. Ochoa, I. et al. BMC Bioinformatics 14, 187 (2013).
14. Hach, F., Numanagic, I., Alkan, C. & Sahinalp, S.C. Bioinformatics 28, 3051-3057 (2012).
15. Christley, S., Lu, Y., Li, C. & Xie, X. Bioinformatics 25, 274-275 (2009).
16. Janin, L., Rosone, G. & Cox, A.J. Bioinformatics 30, 24-30 (2014).
17. DePristo, M.A. et al. Nat. Genet. 43, 491-498 (2011).
18. Yu, Y.W., Yorukoglu, D. & Berger, B. in Research in Computational Molecular Biology: 18th Annual International Conference, RECOMB 2014 - Proceedings (ed. Sharan, R.) 385-399 (Springer, 2014).
19. Kelley, D.R., Schatz, M.C. & Salzberg, S.L. Genome Biol. 11, R116 (2010).
20. Grabherr, M.G. et al. Nat. Biotechnol. 29, 644-652 (2011).
21. Cánovas, R., Moffat, A. & Turpin, A. Bioinformatics 30, 2130-2136 (2014).
22. Li, H. et al. Bioinformatics 25, 2078-2079 (2009).
23. Li, H. & Durbin, R. Bioinformatics 26, 589-595 (2010).
24. Langmead, B. & Salzberg, S.L. Nat. Methods 9, 357-359 (2012).