With the release of Auto PeakTrace RP 6.30 we have updated the basecalling parameters used by the free version of PeakTrace to take advantage of the new options available within PeakTrace 6.30. The PeakTrace command line options settings now used are:
-t abi -ft 300 -c -40 -wq 12 20 -xb yes -cb yes -bc pk -ts no -xs 1000 2 -sm 700
These values correspond to the following Auto PeakTrace and Auto PeakTrace RP Option settings.
These settings are designed to optimise the read length and appearance of the trace, but not the detection of polymorphic sites. If you wish to detect polymorphic sites (mixed bases) raise the mixed peak threshold above 25%.