Skip to main content

Table 1 Comparison of Frequency-Weighted Squared Error (FWSE)

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

  

Original

ReQON

GATK

BAQ

Chromosome 10

Replicate 1

69.36

3.61

11.55

13.93

 

Replicate 2

62.89

5.31

14.91

21.76

Chromosome 20

Replicate 1

71.09

3.04

12.28

15.93

 

Replicate 2

64.34

5.82

17.43

24.38

  1. Comparison of FWSE for two cell line replicates between original quality scores reported from the sequencer machine and after recalibration with ReQON, GATK and BAQ. ReQON quality scores have the lowest FWSE values, corresponding to increased accuracy. ReQON does not overfit the model to the training set, shown by the roughly equivalent FWSE values for both the training (chromosome 10) and testing (chromosome 20) sets after recalibration.
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us