Adapter trimming

The CLC Genomics Workbench comes with a set of predefined adapter sequences from the most common kits provided by the high-throughput sequencing vendors. You can easily add or modify the adapters on this list in the preferences:

        Edit | Preferences () | Data

This will display the adapter trim panel as shown in figure 23.2 where each row represents an adapter sequence including the settings used for trimming.

Figure 23.2: Editing the set of adapters for adapter trimming.

At the bottom of the panel, you have the following options:

• Add Default Rows. If you have deleted or changed the pre-defined set of adapters, you can add them to the list using this button (note that they will not replace existing adapters).
• Delete Row. Delete the selected adapter.
• Add Row. Add a new empty row where you can specify your own adapter settings.

All the information in the panel can be edited by clicking or double-clicking. The Strand, Alignment score and Action settings can also be modified when running the trim (see figure 23.8).

• Action to perform when a match is found
• When is there a match?
• Other adapter trimming options