Pregap automates the steps required to process raw data files to sequence files acceptable by the gap assembly program. Traditionally this has been a task performed either by hand or by large sequence management programs such as Squirrel. The aim of pregap is to provide a skeleton program for this automation. As such it is a small, simple script that performs little in the way of checks. However it has been designed to be reasonably robust and data can never be destroyed.
Many of the programs used by pregap have been rewritten. The philosophy behind these programs now 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.
Only one environment variable is required. Please set the PREGAPROOT variable to the directory containing the `system-pregaprc' file. If this file is not found pregap should still be able to function, but in a limited fashion.