De novo assembly output

Stand-alone mapping

The de novo assembly is followed by a step where the reads used to generate the contigs are mapped against the contigs, using them as reference.

This output is called assembly and opens as a table listing all contigs as seen in figure 32.22.

Image denovoassembly_mapping
Figure 32.22: A de novo assembly read mapping.

The information included in the table is:

At the bottom of the table there are three buttons that can be used to open or extract sequences. Select the relevant rows before clicking on the buttons:

Double clicking on a contig name will open the read mapping in split view.

It is possible to open the assembly as an annotation table (using the icon highlighted in figure 32.22). The annotations available in the table are the following (see figure 32.23):

Image denovoassembly_annotations
Figure 32.23: A de novo assembly read mapping seen as annotation table.

Using the menu in the right end side panel, it is possible to select only one type of annotations to be displayed in the table.

Simple contigs

The output is a sequence list of the contigs generated (figure 32.24), that can also be seen as a table and an annotation table as described for the stand-alone read mapping described above.

Image denovoassembly_contigs
Figure 32.24: A de novo assembly read mapping seen as annotation table.