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Pyrobayes: an improved base caller for SNP discovery in pyrosequences

Abstract

Previously reported applications of the 454 Life Sciences pyrosequencing technology have relied on deep sequence coverage for accurate polymorphism discovery because of frequent insertion and deletion sequence errors. Here we report a new base calling program, Pyrobayes, for pyrosequencing reads. Pyrobayes permits accurate single-nucleotide polymorphism (SNP) calling in resequencing applications, even in shallow read coverage, primarily because it produces more confident base calls than the native base calling program.

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Figure 1: Comparison of the error profiles of Pyrobayes and the native 454 base caller.
Figure 2: Comparison of the base qualities assigned by Pyrobayes and the native 454 base caller.

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Acknowledgements

This work was supported by a grant from the US National Human Genome Research Institute (R01 HG003698) to G.T.M. We thank E. Mardis and the 454 production group at the Washington University Genome Sequencing Center for generating the sequence data used in this work, and A. Clark at Cornell University for providing access to the D. melanogaster reads.

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Contributions

A.R.Q., software and algorithm development and data analysis; D.A.S., data fitting and parameter estimation for Bayesian data likelihoods; M.P.S., alignment algorithm development. A.R.Q. and G.T.M. designed the experiment and wrote the manuscript.

Corresponding author

Correspondence to Gábor T Marth.

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Supplementary Figures 1–5, Supplementary Methods (PDF 423 kb)

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Quinlan, A., Stewart, D., Strömberg, M. et al. Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat Methods 5, 179–181 (2008). https://doi.org/10.1038/nmeth.1172

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