All the data processing other than visual inspection of traces and report generation is handled by the program pregap4 (see section Pregap4 introduction). Pregap4 achieves this by running a set of individual programs selected by the user.
Figure 10. The pregap4 Configure Modules window showing a typical list of mutation data option selections.
The "Configure Modules" window shown in Figure 10. is used to select which programs to apply to a batch of data, and to configure their usage. On the left is a list of programs and options, with "x" showing the ones that have been selected. If the user clicks on an option name its name is given a blue background and its configurable parameters are shown in the right hand panel to enable the user to alter them. Here "Reference Traces" has been selected which enables the user to set the reference traces and sequence.
The other selected options (marked with "x") are typical of the ones used for mutation detection studies. Below we describe the use of each plus a few alternatives. All of the options are descibed in more detail elsewhere in our documentation, our intention here is to give an overview of their use during mutation studies.
Note that the window labelled "Files to Process" is used to tell the program which files to process as a batch.