We often get asked if the improvement seen by using PeakTrace is real. While this question is best answered by doing your own investigations (try the free version of PeakTrace on your own traces and see), it is something we have investigated in depth.
Determining if a basecaller is accurate and provides real improvement is not a simple process – Ewing & Green had two back-to-back papers in Genome Research answering this very question for phred [1, 2]. We followed the same approach to validate both PeakTrace and KB. This study found that PeakTrace not only offered significantly more alignable Q20+ and total bases than KB, it was also more accurate at predicting the true error rate than KB [3].
While this study was performed using an earlier version of PeakTrace (4.25) and KB (1.2), it underestimates the benefits of using PeakTrace. Since 2010 PeakTrace has continued to improve, while the most recent release of KB (1.4.1) provides basically the same read length as KB 1.2.
References
- Ewing B, Hillier L, Wendl MC, Green P. (1998). Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185.
- Ewing B, & Green P. (1998): Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186-194.
- Tillett, D. (2010). Validation of the PeakTrace basecaller.