Specify, Save, and Apply Parameters

To customize parameters used in assembly and downstream analysis:

Choose Project > Project Parameters > Edit Parameters. The Project Parameters popup opens at the Consensus parameters screen. Five additional parameter screens can be accessed by clicking their names on the left of the popup.

Each parameter screen is described in a separate topic:

• Consensus
• Strategy Viewing and Coverage
• Pair Specifier
• Assembly
• End Trimming
• Variant Discovery

To save customized parameters and manually apply them to other projects:

1. Customize the five parameters screens as desired.

2. Choose Project > Project Parameters > Save Parameters.

3. Select a location and file name for the parameter set. The parameters are saved in .spp format.

4. Open a different project in SeqMan Ultra or create a new project. Choose Project > Project Parameters > Apply Parameters. The customized parameters are applied to the project. You can also share the file with colleagues so they can apply the parameter set to their own projects.

You can use this method to save different sets of parameters to apply in different situations.

To save customized parameters as the default set for future projects:

1. Customize the five parameters screens as desired.

2. Choose Project > Project Parameters > Save Parameters as Default.

Future projects will use this parameter set by default. You can still change individual parameters by making new selections in the five screens or by using the Project > Project Parameters > Apply Parameters command described above to apply a saved set of parameters.

To quickly apply recently-saved parameters:

Choose Project > Project Parameters > Apply Parameters > (file name).

To restore the original DNASTAR parameters:

Choose Project > Project Parameters > Restore DNASTAR Default Parameters.