DOI: 10.1101/gr.8.3.186. Base-Calling of Automated Sequencer Traces Using <i>Phred.</i> II. Error Probabilities

Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities

10.1101/gr.8.3.186

Crossref journal-article

Cold Spring Harbor Laboratory

Genome Research (246)

Abstract

Elimination of the data processing bottleneck in high-throughput sequencing will require both improved accuracy of data processing software and reliable measures of that accuracy. We have developed and implemented in our base-calling program phred the ability to estimate a probability of error for each base-call, as a function of certain parameters computed from the trace data. These error probabilities are shown here to be valid (correspond to actual error rates) and to have high power to discriminate correct base-calls from incorrect ones, for read data collected under several different chemistries and electrophoretic conditions. They play a critical role in our assembly program phrap and our finishing programconsed.

Bibliography

Ewing, B., & Green, P. (1998). Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities. Genome Research, 8(3), 186â194.

Authors 2

Brent Ewing (first)
Phil Green (additional)

References 8 Referenced 3,670

10.1101/gr.6.2.80
Ewing, B., L. Hillier, M. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res. (this issue). (10.1101/gr.8.3.175)
10.1093/nar/21.19.4530
Golden J.B. Torgersen D. Tibbetts C. (1993) Pattern recognition for automated DNA sequencing: I. On-line signal conditioning and feature extraction for basecalling. in Proceedings of the First International Conference on Intelligent Systems for Molecular Biology, eds Hunter L. Searls D. Shavlick J. (AAAI Press, Menlo Park, CA), pp 136–144.
Gordon, D., C. Abajian, and P. Green. 1998. Consed: A graphical tool for sequence finishing. Genome Res. (this issue). (10.1101/gr.8.3.195)
10.1093/nar/22.7.1272
10.1093/nar/20.10.2471
10.2144/96214rr02 / BioTechniques / AmpliTaq DNA polymerase, FS dye-terminator sequencing: Analysis of peak height patterns. by Parker (1996)

Dates

Type	When
Created	10 years ago (Aug. 5, 2015, 8:34 p.m.)
Deposited	3 years, 9 months ago (Nov. 18, 2021, 1:37 p.m.)
Indexed	6 hours, 9 minutes ago (Aug. 31, 2025, 7:12 p.m.)
Issued	27 years, 6 months ago (March 1, 1998)
Published	27 years, 6 months ago (March 1, 1998)
Published Online	27 years, 6 months ago (March 1, 1998)
Published Print	27 years, 6 months ago (March 1, 1998)

Funders 0

None

BibTeX

@article{Ewing_1998, title={Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities}, volume={8}, ISSN={1549-5469}, url={http://dx.doi.org/10.1101/gr.8.3.186}, DOI={10.1101/gr.8.3.186}, number={3}, journal={Genome Research}, publisher={Cold Spring Harbor Laboratory}, author={Ewing, Brent and Green, Phil}, year={1998}, month=mar, pages={186–194} }

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