The core transforms of the DITA Toolkit represent the " Reference Implementation" for processing the standard DITA specification as maintained by OASIS Open.
A pre-process is done before the main transformation. The input of Pre-process is dita files and the output of Pre-process is also dita files. But the output is in temp directory. Pre-process is the basic for the main transformation, it handles several different processing before the main transformation. Without pre-process, dita topics and map can still be transformed into different outputs, but the features in pre-process such as resolving conref attribute are not available.
The complete transformation including pre-process can be excuted by the ant script. There are some examples of simple ant script in directory /ant. The ant target for the transformation which can be called is listed at Running Ant