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. Access through your

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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. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Department of

Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, 02467, Massachusetts, USA Aaron R Quinlan, Donald A Stewart, Michael P Strömberg & Gábor T Marth Authors * Aaron R

Quinlan View author publications You can also search for this author inPubMed Google Scholar * Donald A Stewart View author publications You can also search for this author inPubMed Google

Scholar * Michael P Strömberg View author publications You can also search for this author inPubMed Google Scholar * Gábor T Marth View author publications You can also search for this

author inPubMed Google Scholar 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. SUPPLEMENTARY INFORMATION

SUPPLEMENTARY TEXT AND FIGURES Supplementary Figures 1–5, Supplementary Methods (PDF 423 kb) RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE 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 Download

citation * Received: 03 October 2007 * Accepted: 04 December 2007 * Published: 13 January 2008 * Issue Date: February 2008 * DOI: https://doi.org/10.1038/nmeth.1172 SHARE THIS ARTICLE Anyone

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