Use the Configure Modules tab (highlighted in oval) to switch to configuration options. Check/Uncheck the crosses next to the modules to resemble the picture presented above.
When you select Gap4 shotgun assembly module you are required to supply a name for your new database (highlighted in square) which will be used to store all the information.
Click Run button (highlighted in diamond)
The Pregap will preprocess the files and display the chromatogram. The parts of the sequence marked for quality clipping will be highlighted. You can view and check your chromatograms for the following problems.
How clean is your sequence? Are the peaks evenly-spaced and is there baseline 'noise'?
Low baseline noise.
Higher baseline noise
High baseline noise
Mis-spaced peaks or double-peaks
Loss of resolution
Homopolymeric stretches
