How to run Extend Contigs

        Toolbox | Genome Finishing Module (Image finishing_tools_folder) | Extend Contigs (Image contig_extender_16_n_p)

This opens the dialog shown in figure 11.3 where at least one assembly must be selected.

Image contig_extender_step1
Figure 11.3: Select de novo assembly.

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.

Image contig_extender_step2
Figure 11.4: Specify parameters for deciding how much the contig should be extended.

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.