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

BMC Bioinformatics

Christopher R Cabanski⁵  Keary Cavin³  Chris Bizon³  Matthew D Wilkerson¹  Joel S Parker⁴  Kirk C Wilhelmsen⁴  Charles M Perou⁴  JS Marron¹  D Neil Hayes² 

[1] Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA

[2] Department of Internal Medicine, Division of Medical Oncology, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

[3] Renaissance Computing Center, Chapel Hill, NC, USA

[4] Department of Genetics, Chapel Hill, NC, USA

[5] Department of Statistics and Operations Research, Chapel Hill, NC, USA

关键词: Bioconductor;    Bioinformatics;    Recalibration;    Quality score;    Next-generation sequencing;   

Others  :  1088149
DOI  :  10.1186/1471-2105-13-221

 received in 2012-05-04, accepted in 2012-08-22,  发布年份 2012

【 摘 要 】

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.

【 授权许可】

   
2012 Cabanski et al.; licensee BioMed Central Ltd.

【 图 表 】

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