Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects

Scientific Reports

Volumn 3, Issue , 2013, Pages

  Farrer, Rhys A ^a   Henk, Daniel A ^a   MacLean, Dan ^b   Studholme, David J ^c   Fisher, Matthew C ^a  

^a ST MARY S HOSPITAL   (United Kingdom)

^b SAINSBURY LABORATORY   (United Kingdom)

^c UNIVERSITY OF EXETER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; FUNGAL GENOME; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; GENOME, FUNGAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 84875767941     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep01512     Document Type: Article

References (31)

1. DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
2. The 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 (2010).
3. Kiezun, A. et al. Exome sequencing and the genetic basis of complex traits. Nat. Genet., 44, 623-630 (2012).
4. Aird, D. et al. Analyzing and minimizing PCR amplification bias in Illumina Sequencing libraries. Genome Biol. 12, R18 (2011).
5. Sasson, A. & Michael1, T. P. Filtering error from SOLiD Output. Bioinformatics 26, 849-850 (2010).
6. Huse, S. M., Huber, J. A.,Morrison, H. G., Sogin, M. L. &Welch, D. M. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 8, R143 (2007).
7. Landan, G. & Graur, D. Characterization of pairwise and multiple sequence alignment errors. Gene 441, 141-7 (2009).
8. Flicek, P. & Birney, E. Sense from sequence reads: methods for alignment and assembly. Nature Methods 6, S6-12 (2009).
9. Alkan, C., Sajjadian, S. & Eichler, E. E. Limitations of next-generation genome sequence assembly. Nat. Methods 8, 61-65 (2011).
10. Frith, M. C., Hamada, M. & Horton, P. Parameters for accurate genome alignment. BMC Bioinformatics 2010, 11, 80 (2010).
11. Li, H.& Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-60 (2009).
12. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biology 10, R25 (2009).
13. Burrows, M. & Wheeler, D. J. A block-sorting lossless data compression algorithm. Technical report 124. Palo Alto, CA: Digital Equipment Corporation (1994).
14. Rumble, S. M. et al. SHRiMP: Accurate Mapping of Short Color-space Reads. PLoS Computational Biology 5 (2009).
15. Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851-8 (2008).
16. Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966-7 (2009).
17. Lin, H., Zhang, Z., Zhang, M. Q., Ma, B. & Li, M. ZOOM! Zillions of oligos mapped. Bioinformatics 24, 2431-7 (2008).
18. Li, H. & Homer, N. A survey of sequence alignment algorithms for nextgeneration sequencing. Briefings in Bioinformatics 11, 473-483 (2010).
19. Kelley, D. R., Schatz, M. C. & Salzberg, S. L. Quake: quality-aware detection and correction of sequencing errors. Genome Biology 11, R116 (2010).
20. Zhao, X. et al. EDAR: an efficient error detection and removal algorithm for next generation sequencing data. J. Comput. Biol. 17, 1549-60 (2010).
21. Ruffalo, M., LaFramboise, T. & Koyutürk, M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics 27, 2790-6 (2011).
22. McKenna, A. et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20, 1297-1303 (2010).
23. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-9 (2009).
24. Farrer, R. A., Kemen, E., Jones, J. D. & Studholme, D. J. De novo assembly of the Pseudomonas syringae pv. Syringae B728a genome using Illumina/Solexa short sequence reads. FEMS Microbiol. Lett 1, 103-111 (2009).
25. Miller, M. J. & Powell, J. I. A quantitative comparison of DNA sequence assembly programs. J. Comput. Biol. 1, 257-69 (1994).
26. Zhang, W. et al. A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies. PLoS One 6 (2011).
27. Salmela, L. Correction of sequencing errors in amixed set of reads. Bioinformatics 26, 1284-90 (2011).
28. Raffaele, S. et al. Genome evolution following host jumps in the Irish potato famine pathogen lineage. Science. 330, 1540-3 (2010).
29. Farrer, R. A. et al. Multiple emergence of genetically diverse amphibian-infecting chytrids include a globalised hypervirulent lineage. Proc. Natl. Acad. Sci. U.S.A. 108, 18732-6 (2011).
30. Musumeci, L. et al. Single nucleotide differences (SNDs) in the dbSNP database may lead to errors in genotyping and haplotyping studies. Human mutation 31, 67-73 (2010).
31. Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156-8 (2011).