One of the most commonly misunderstood options of the PeakTrace™ Basecaller is stealth mode. The specification of the .phd.1 and .scf file requires that the basecaller and trace processor used are recorded. If PeakTrace is used then PeakTrace should be noted in these files (Figure 1).
Figure 1. .phd.1 file generated by PeakTrace when not using stealth mode.
If stealth mode is selected then the trace processor and basecaller recorded within the .phd.1 and .scf files will be KB™ 1.4, hiding that the trace was processed with PeakTrace (Figure 2).
Figure 2. .phd.1 file generated using stealth mode.
Why use Stealth Mode?
We would prefer that nobody uses stealth mode. Not only is it misleading, it avoid end users knowing that they have got a better trace from their facility using PeakTrace.
The reason why we offer this mode is that one of the major benefits of PeakTrace for commercial users is that it provides a huge competitive advantage over other Sanger DNA sequencing facilities that only use the KB Basecaller – the end user gets more accurate basecalling, longer reads and improved trace chromatograms. Stealth mode allows commercial users to maintain this competitive advantage without letting the competition know how they are able to win so much new business. The bottom line is that this is a feature requested by our customers (the DNA sequencing facilities), not one that we want anyone to use.
Having said this, if your competitors are so keen for you to not find out about PeakTrace then maybe it is a very good idea to investigate what PeakTrace can do. The facilities using PeakTrace are not doing so because they like to waste money, they are doing it because every time one of your customers sees the quality of the sequencing data they switch to their service. The good news is you can use PeakTrace too.