The Scans tab is used to set scanning parameters. The tab can be accessed in either of two ways:
- From the Assembly Options screen, click the Advanced Options button then click on the Scans tab.
- From the Preassembly Options screen, click the Advanced Options button then click on the Scans tab.
Default parameters vary according to the sequencing technology and project type specified elsewhere in the wizard, and values seldom need to be changed.
| Section | Parameter | Description |
|---|---|---|
| Vector/Adaptor scan section | Mer length | The minimum length of a mer required to be considered an exact match when searching for vector. |
| Trim length | The minimum length required for a mer to be considered as a match for vector trimming. | |
| Minimum matches | The minimum number of matching mers required to start an alignment. | |
| Trim to end | The distance to the endpoint where trimming will go all the way to the end of the sequence. | |
| Repeat scan section | Mer length | The minimum length of a mer required to be considered an exact match when scanning for repeats. |
| Flag length | The minimum length required for a mer to be flagged as a repeat. | |
| Minimum matches | The minimum number of matching mers required to be considered a repeat. | |
| Contaminant scansection | Mer length | The minimum length of a mer required to be considered an exact match when scanning for contaminants. |
| Minimum matches | The minimum number of matching mers required to mark the sequence as a contaminant. |
Once you are finished, click the Alignment, Layout or Trimming tabs (if you came via Assembly Options) or the Trimming or Alignment tabs (if you came through Preassembly Options) to change those settings. Or click OK to save all changes and return to the Assembly Options or Pressembly Options screens.
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