title: ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Statistics and Operations Research, Chapel Hill, NC, USA.
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Cabanski
authors.forename: Keary
authors.initials: K
authors.lastname: Cavin
authors.forename: Chris
authors.initials: C
authors.lastname: Bizon
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Wilkerson
authors.forename: Joel S
authors.initials: JS
authors.lastname: Parker
authors.forename: Kirk C
authors.initials: KC
authors.lastname: Wilhelmsen
authors.forename: Charles M
authors.initials: CM
authors.lastname: Perou
authors.forename: J S
authors.initials: JS
authors.lastname: Marron
authors.forename: D Neil
authors.initials: DN
authors.lastname: Hayes
mesh_terms: D002138:Calibration; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000592:standards*; D016015:Logistic Models; D016415:Sequence Alignment; D012984:Software