When using the Extend Contigs tool to create larger overlaps between contigs, these overlaps remain unless the contigs are actually joined. In the process of joining, the overlapping nucleotides are reduced to only being included once. However, extended ends of contigs not forming part of a join will remain. The Remove Extension of Contigs tool removes extensions that were not included in a join.
See figure 13.1 for an example of an overlap of a contig that should be removed if the region isn't included in a join.
Figure 13.1: Overlap between contig 14 and contig 98 that was created when the selected region was extended. If these two contigs aren't joined, the overlap region will include some nucleotides twice.