Before assembly into Gap4 the raw data from sequencing instruments needs to pass through several steps, such as sequencing vector removal, quality evaluation, and conversion of data formats. These can be seen in the figure on the following page. Each of these steps is performed by a small individual program. Pregap is used to pass a batch of readings through these steps in an automatic way.
The philosophy behind the separate programs that pregap uses is that each separate task (eg creation of SCF file, clipping and vector screening) should be performed by a separate program. This allows for easy maintenance and allows the users to replace any stage with their own programs. Please refer to the relevant sections of the package manual for descriptions of each program used.
Automation in pregap is achieved by means of `.pregaprc' files. Pregap asks several questions, but only if the answers are not already known. These answers can be stored in the `.pregaprc' files. These files may also contain additional information which is used by Pregap but considered optional (and hence will not be asked for). It is worth pointing out that to use Pregap it is not essential to create `.pregaprc' files, however it is worth spending time to learn this process if it is used on a frequent basis.
Gap4 can make use of information about your readings which may not be contained within the raw data files, such as sequencing chemistry and whether it is a forward or reverse reading. Once again this is not essential, but if it is relevant and known Gap4 can provide many additional features. This information is generally passed into Gap4 by use of Pregap's `.pregaprc' files. This may seem a somewhat labourious task but it is worth noting that you should be storing this information somewhere if only for your own records. If you adhere to a rigid naming conventions it may be possible to avoid much of the work involved here. The section on naming conventions (see section Naming Conventions) explains this in more detail.