PeakTrace 6 is the latest version of the PeakTrace Basecaller™ software family. It combines improved basecalling and trace processing with the QualTrace III quality control software. The new features of PeakTrace 6 include:
PeakTrace 6 offers improved basecalling compared to earlier versions of PeakTrace and as expected the KB basecaller.
Figure 1 show an example of ABI 3730 trace at base 1000 that was basecalled with KB 1.4.1, PeakTrace 5.80 and PeakTrace 6.00. Figure 2 shows an BLAST alignment of the PeakTrace 6 basecalled trace with the consensus (true) sequence shows no errors before base 1079. Note the basecalling error made by KB where the 3Gs just before base 990 are called as 2Gs and both of these are given erroneous high quality scores.
A. KB Basecaller
B. PeakTrace 5.80 Basecaller
C. PeakTrace 6.00 Basecaller
Figure 1. A comparison of KB, PeakTrace 5.80 and PeakTrace 6.00. The same trace is shown basecalled with each of the three different basecallers.
Figure 2. BLAST alignment of the PeakTrace 6.00 basecalled sequence with the true sequence. Query: PeakTrace 6.00 basecalled sequence; Sbjct: True sequence.
Improved Trace Appearance
PeakTrace 6 offers new options to improve the appearance of trace files. While not affecting basecalling quality, two new options (clean baseline and extra normalization) provide better looking traces with reduced baseline noise. These two settings can also be applied to KB basecalled traces to improve their appearance.
A. Default PeakTrace 6 basecalling
B. PeakTrace 6 + clean baseline + extra normalization
Figure 3. Examples of PeakTrace 6 basecalling with and without use of the clean baseline and extra normalisation. A. Default settings. B. Clean baseline + extra normalization.
QualTrace III and Trace Quality Reports
PeakTrace 6 incorporates an improved version of the QualTrace II Quality Control Software that provides additional feedback on the quality and potential production or sequencer issues. QualTrace III provides feedback on 47 parameters of the DNA sequencer and template quality that can be used to track production quality over time. In addition, PeakTrace 6 can generate text based files of the QualTrace III data (Trace Reports) that can be supplied to end users giving them feedback on why their data is below their expectations and what they might want to change to get better data.
Upgrading to PeakTrace 6
PeakTrace 6 is a free upgrade for all current users of PeakTrace. Current users of Auto PeakTrace and the Linux PeakTrace Basecaller requires a PeakTrace 6 license update. Users of Auto PeakTrace RP will need to update the software, but the current license will continue to work. To update please contact Nucleics (or your local supplier).
To learn more about PeakTrace 6 please see the PeakTrace Overview page, PeakTrace FAQ page or download the Auto PeakTrace Users Manual. We have also started a series looking at the new features of PeakTrace 6 in depth.