cap2program to perform shotgun assembly. Output will be placed in the fofn.assembly directory, where fofn is the filename prefix listed in the "Files to Process" panel. The output is in a format suitable for directed assembly within Gap4. This can also be performed by using the "Enter Assembly into Gap4" module. Cap2 is not included as part of the Staden Package. It is available from Xiaoqiu Huang (email@example.com). There are no adjustable parameters for this module.