To specify the values for the Sequence Condensation step
1. Click Next or Condensation.
The Condensation Settings page opens. The Reference Length options vary depending on the selected Application Type—de novo Assembly, or all application types other than de novo Assembly.
 | For a detailed discussion of the Sequence Condensation tool and its settings, see Sequence Condensation Tool. |
2. On the Condensation Type dropdown list, for Illumina data, SOLiD System data, or Ion Torrent data, select the condensation method that you are using (Consolidation, Elongation, or Error Correction.)
| | For Roche/454 data, Error Correction is the only available method and the Condensation Type field is automatically set to this value. |
3. For for Illumina data, SOLiD System data, or Ion Torrent data, click Inspect Input Files. For Roche data, go to Step 4.
The NextGENe Project Wizard scans your data file and sets a variety of default values for the general sequence condensation settings. You can modify these values if needed. See Sequence Condensation Tool - General Settings.
| | If you load multiple sample files for analysis, all the data is evaluated as whole, not by individual sample files. |
4. Click Open Advanced Settings.
• For the Roche/454 instrument type, the advanced settings are unique and are populated with values that SoftGenetics has determined, from experience, are appropriate for most datasets for the instrument.
• For the Illumina, SOLiD, and Ion Torrent instrument types, the available settings are the same and the advanced settings are populated based on the Read Lengths and Expected Depth of Coverage values that were set in Step 3.
5. Leave the default values as-is, or make any changes as needed. See one of the following:
6. If applicable, continue to the next analysis step for the project; otherwise, if this is your last analysis step, click Finish, and then continue to To finish the project.