Toolbox | Genome Finishing Module () | Extend Contigs ()
This opens the dialog shown in figure 11.3 where at least one assembly must be selected.
If a read mapping is chosen rather than a de novo result, the extended contig will consist of the reference sequence being extended. Click Next.
The next step in figure 11.4 shows the parameters which controls when the extension of the contig should stop in cases where the number of supporting reads is too low or the fraction of unaligned ends is too high.
After clicking Finish in the Result handling step, the contigs will be extended if possible. To see the results of the contig extension and to join the contigs that now are overlapping, run the Align Contigs tool again on the extended assembly.