PyroHMMvar: A sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data

Bioinformatics

Volumn 29, Issue 22, 2013, Pages 2859-2868

  Zeng, Feng ^a   Jiang, Rui ^a   Chen, Ting ^a,b  

^a TSINGHUA UNIVERSITY   (China)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIPLOIDY; DNA SEQUENCE; GENOTYPING TECHNIQUE; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN GENOME; PROBABILITY; PROCEDURES; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; ARTICLE; METHODOLOGY;

DIPLOIDY; GENOME, HUMAN; GENOTYPING TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MARKOV CHAINS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 84890059133     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt512     Document Type: Article

References (34)

1. Abecasis, G.R. et al. (2012) An integrated map of genetic variation from 1, 092 human genomes. Nature, 491, 56-65.
2. Albers, C.A. et al. (2011) Dindel: accurate indel calls from short-read data. Genome Res., 21, 961-973.
3. Balzer, S. et al. (2010) Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim. Bioinformatics, 26, i420-i425.
4. Bhangale, T.R. et al. (2005) Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum. Mol. Genet., 14, 59-69.
5. Chen, Y. et al. (2009) PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics, 25, 2514-2521.
6. Chin, C.S. et al. (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods, 10, 563-569.
7. Dempster, A.P. et al. (1977) Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. Series B Methodol., 39, 1-38.
8. DePristo, M.A. et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet., 43, 491-498.
9. Durbin, R. et al. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK.
10. Emde, A.K. et al. (2012) Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics, 28, 619-627.
11. Homer, N. et al. (2009) BFAST: an alignment tool for large scale genome resequencing. PLoS One, 4, e7767.
12. Huse, S.M. et al. (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol., 8, R143.
13. Iqbal, Z. et al. (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat. Genet., 44, 226-232.
14. Kofler, R. et al. (2009) PanGEA: identification of allele specific gene expression using the 454 technology. BMC Bioinformatics, 10, 143.
15. Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
16. Levy, S. et al. (2007) The diploid genome sequence of an individual human. PLoS Biol., 5, e254.
17. Li, H. (2011) Improving SNP discovery by base alignment quality. Bioinformatics, 27, 1157-1158.
18. Li, H. (2012) Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics, 28, 1838-1844.
19. Li, H. and Durbin, R. (2010) Fast and accurate long-read alignment with Burrows- Wheeler transform. Bioinformatics, 26, 589-595.
20. Li, H. et al. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18, 1851-1858.
21. Li, R. et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966-1967.
22. Li, S. et al. (2013) SOAPindel: efficient identification of indels from short paired reads. Genome Res., 23, 195-200.
23. Margulies, M. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
24. Marth, G.T. et al. (1999) A general approach to single-nucleotide polymorphism discovery. Nat. Genet., 23, 452-456.
25. Mills, R.E. et al. (2006) An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res., 16, 1182-1190.
26. Nielsen, R. et al. (2011) Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet., 12, 443-451.
27. Ning, Z. et al. (2001) SSAHA: a fast search method for large DNA databases. Genome Res., 11, 1725-1729.
28. Rothberg, J.M. et al. (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature, 475, 348-352.
29. Rumble, S.M. et al. (2009) SHRiMP: accurate mapping of short color-space reads. PLoS Comput. Biol.,, 5, e1000386.
30. Shen, Y. et al. (2010) A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res., 20, 273-280.
31. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
32. Vacic, V. et al. (2008) A probabilistic method for small RNA flowgram matching. Pac. Symp. Biocomput., 75-86.
33. Wheeler, D.A. et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature, 452, 872-876.
34. Zeng, F. et al. (2013) PyroHMMsnp: an SNP caller for Ion Torrent and 454 sequencing data. Nucleic Acids Res., 41, e136.