The Layout tab of the Preassembly Options dialog is used to set parameters for the layout phase of the assembly. To access the tab from the Preassembly Options screen, click the Advanced Assembly Options button then click on the Layout tab.

Default parameters vary according to the sequencing technology and project type specified elsewhere in the wizard, and values seldom need to be changed.

Parameter Description
Repeat handing Check this option to enable the choice between automatic or manually-specified thresholds for dealing with repeated sequence. If you check this box, you will need to specify either Auto-calculate mer count thresholds or Set mer count thresholds. If you choose the latter, you need to enter minimum and maximum values in the boxes on the right.
Mer size Choose whether to use Automatic or Custom mer size thresholds for the first pass, and optionally, the second pass. If you choose Custom, you need to enter a threshold for First pass. If you wish to do a second pass, check Second pass and enter a threshold for that pass as well.
Max overhang The maximum allowed length of the sum of the two overhang regions.
Min match length The minimum length of at least one aligned segment of a read after trimming. The default value varies depending on the read technology you selected. Allowed values are 0-999.
Min match length ratio The minimum allowable overlap to read length ratio.
Max offset between mer matches The maximum offset in bases from the main matching diagonal for a given mer match.
Use chimeric read detection Checking the box enables a method to identify artifactual chimeric reads in the data set.
Max overhang ratio The maximum allowable overhang to overlap length ratio.
Max gap between mer matches The theoretical maximum length of a gap that could be inserted between mer matches. In practice, the maximum gap size will usually be about half of this value. The maximum allowable value is 99
Max mismatch percentage The maximum value of the estimated percentage of mismatching bases in the overlap based on the estimated sequencing error rate.

Once you are finished, click the Alignment tab to change settings there, or click OK to save changes and return to the Pressembly Options screen.

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