Before entry into a gap4 database the raw data from sequencing instruments needs to be passed through several processes, such as screening for vectors, quality evaluation, and conversion of data formats. Pregap4 is used to pass a batch of readings through these steps in an automatic way. It provides an interface for setting up and configuring the processing and for controlling the passage of the readings through each stage. The separate tasks are termed "modules" and each module is typically managed by a dedicated program. Pregap4 wraps all of these modules into a single easy to use environment, whilst maintaining the flexibility to select and extend the processing modules. It is an, as yet, unpublished replacement of the program pregap Bonfield, J.K. and Staden, R. Experiment files and their application during large-scale sequencing projects. DNA Sequence 6, 109-117 (1996).