Any weak regions are tagged and the Dock program is run to automatically pick and order primers for all non-vector ends and to surround any regions tagged as weak. The List Manager records all the finishing reads done for a project, the success rate of those reads, the number of primers needed to finish the project, and other relevant finishing statistics.
Mapper draws the relationships between contigs, as shown below.
Progress is easily monitored by the Gap4 quality display below which shows the remaining edits to be made in red, and any remaining single stranded regions in blue and green. Usually there will be one more list of data requested from the lab at this step.