ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data

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Creator
  • Cabanski, Christopher R
    • Affiliation: College of Arts and Sciences, Department of Statistics and Operations Research
  • Cavin, Keary
    • Affiliation: Renaissance Computing Institute
  • Bizon, Chris
    • Affiliation: Renaissance Computing Institute
  • Wilkerson, Matthew D
    • Affiliation: N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center
  • Parker, Joel
    • Affiliation: N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center
  • Wilhelmsen, Kirk
    • Affiliation: N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center
  • Perou, Charles
    • Affiliation: N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center
  • Marron, JS
    • Affiliation: N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center
  • Hayes, D
    • Affiliation: N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center
Abstract
  • Background Next-generation sequencing technologies have become important tools for genome-wide studies. However, the quality scores that are assigned to each base have been shown to be inaccurate. If the quality scores are used in downstream analyses, these inaccuracies can have a significant impact on the results. Results Here we present ReQON, a tool that recalibrates the base quality scores from an input BAM file of aligned sequencing data using logistic regression. ReQON also generates diagnostic plots showing the effectiveness of the recalibration. We show that ReQON produces quality scores that are both more accurate, in the sense that they more closely correspond to the probability of a sequencing error, and do a better job of discriminating between sequencing errors and non-errors than the original quality scores. We also compare ReQON to other available recalibration tools and show that ReQON is less biased and performs favorably in terms of quality score accuracy. Conclusion ReQON is an open source software package, written in R and available through Bioconductor, for recalibrating base quality scores for next-generation sequencing data. ReQON produces a new BAM file with more accurate quality scores, which can improve the results of downstream analysis, and produces several diagnostic plots showing the effectiveness of the recalibration.
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Resource type
  • Article
Rights statement
  • In Copyright
Rights holder
  • Christopher R Cabanski et al.; licensee BioMed Central Ltd.
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Journal title
  • BMC Bioinformatics
Journal volume
  • 13
Journal issue
  • 1
Page start
  • 221
Language
  • English
Is the article or chapter peer-reviewed?
  • Yes
ISSN
  • 1471-2105
Bibliographic citation
  • BMC Bioinformatics. 2012 Sep 04;13(1):221
Publisher
  • BioMed Central Ltd
Access right
  • Open Access
Date uploaded
  • September 19, 2012

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