Using state machines to model the Ion Torrent sequencing process and to improve read error rates

Bioinformatics

Volumn 29, Issue 13, 2013, Pages

  Golan, David ^a   Medvedev, Paul ^b  

^a TEL AVIV UNIVERSITY   (Israel)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOLOGICAL MODEL; DNA SEQUENCE; PROCEDURES; ARTICLE; METHODOLOGY;

ALGORITHMS; MODELS, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 84879981084     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt212     Document Type: Conference Paper

References (15)

1. Balzer, S. et al. (2010) Characteristics of 454 pyrosequencing data - enabling realistic simulation with flowsim. Bioinformatics, 26, i420-i425.
2. Baum, L. and Petrie, T. (1966) Statistical inference for probabilistic functions of finite state markov chains. Ann. Math. Stat., 37, 1554-1563.
3. Beuf, K. et al. (2012) Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model. BMC Bioinformatics, 13, 303.
4. Durbin, R. et al. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK.
5. Eisenstein, M. (2012) The battle for sequencing supremacy. Nat. Biotechnol., 30, 1023-1026.
6. Hopcroft, J.E. and Ullman, J.D. (1979) Introduction to Automata Theory, Languages and Computation. Addison-Wesley, Reading, MA, USA.
7. Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
8. Ledergerber, C. and Dessimoz, C. (2011) Base-calling for next-generation sequencing platforms. Brief. Bioinform., 12, 489-497.
9. Lysholm, F. et al. (2011) FAAST: Flow-space assisted alignment search tool. BMC Bioinformatics, 12, 293.
10. Merriman, B. et al. (2012) Progress in Ion Torrent semiconductor chip based sequencing. Electrophoresis, 33, 3397-3417.
11. Quail, M. et al. (2012) A tale of three next generation sequencing platforms: Comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics, 13, 341.
12. Quince, C. et al. (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics, 12, 38.
13. Quinlan, A.R. et al. (2008) Pyrobayes: An improved base caller for SNP discovery in pyrosequences. Nat. Methods, 5, 179-81.
14. Rothberg, J.M. et al. (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature, 275, 348-352.
15. Vacic, V. et al. (2008) A probabilistic model for small RNA flowgram matching. In: Pacific Symposium on Biocomputing. pp. 75-86.