Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Base-calling of automated sequencer traces using phred. II. Error probabilities

B Ewing1, P Green

  • 1Department of Molecular Biotechnology, University of Washington, Seattle, Washington 98195-7730, USA.

Genome Research
|May 16, 1998
PubMed
Summary

High-throughput sequencing requires accurate data processing. A new error probability estimation in the phred software improves base-call accuracy and reliability across various sequencing conditions.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Inclusive Search for Anomalous Single-Photon Production in MicroBooNE.

Physical review letters·2026
Same author

First Search for Dark Sector e^{+}e^{-} Explanations of the MiniBooNE Anomaly at MicroBooNE.

Physical review letters·2026
Same author

First Measurement of Charged-Current Muon-Neutrino-Induced K^{+} Production on Argon Using the MicroBooNE Detector.

Physical review letters·2026
Same author

Search for an Anomalous Production of Charged-Current ν_{e} Interactions without Visible Pions across Multiple Kinematic Observables in MicroBooNE.

Physical review letters·2025
Same author

First Measurement of ν_{e} and ν[over ¯]_{e} Charged-Current Single Charged-Pion Production Differential Cross Sections on Argon Using the MicroBooNE Detector.

Physical review letters·2025
Same author

First Double-Differential Cross Section Measurement of Neutral-Current π^{0} Production in Neutrino-Argon Scattering in the MicroBooNE Detector.

Physical review letters·2025

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • High-throughput sequencing generates large datasets, creating data processing bottlenecks.
  • Accurate base-calling is crucial for reliable downstream genomic analysis.
  • Existing software lacks robust measures for base-call accuracy.

Purpose of the Study:

  • To develop and implement a method for estimating base-call error probabilities.
  • To validate the accuracy and discriminatory power of these error probabilities.
  • To integrate error probability estimation into existing sequencing software.

Main Methods:

  • Implemented error probability estimation within the phred base-calling program.
  • Utilized trace data parameters to compute error probabilities.

Related Experiment Videos

  • Validated error probabilities against actual error rates using diverse sequencing data.
  • Assessed the power of error probabilities to distinguish correct from incorrect base-calls.

    • Main Results:

    • The developed error probabilities accurately reflect actual base-call error rates.
    • Error probabilities effectively discriminate between correct and incorrect base-calls.
    • The method is robust across different sequencing chemistries and electrophoretic conditions.
    • These probabilities are critical for the phrap assembly and consed finishing programs.

    Conclusions:

    • The phred program now provides reliable error probabilities for each base-call.
    • This advancement addresses a key bottleneck in high-throughput sequencing data processing.
    • The validated error probabilities enhance the accuracy of downstream genomic assembly and finishing.