The Layout tab of the Assembly Options dialog is used to set parameters for the layout phase of the assembly. To access the tab from the Assembly Options screen, click the Advanced Options button then click on the Layout tab. The options available in this tab may vary depending on the workflow.

Parameter Description
Alignment-based layout refinement If you are following a whole-genome workflow, checking this button may improve the accuracy of the assembly.
Layout Stringency Choose from the following:

  • High – Recommended for whole genomes.

  • Low – Recommended for all other workflows.

  • Custom – If you wish to enter the Minimum layout length manually. This is the minimum number of identical matching bases (from the mer analysis only) for a read to be included in the layout. It is specified by an integer, with a default of 50 nucleotides. For reads shorter than 100 bases, the setting is automatically adjusted to the mer size. Increasing this number decreases the false discovery rate (FDR) and true positive rate (TPR). Allowed values are 0-999. The default is -1 nt (nucleotides).

Once you are finished, click the Alignment or Trimming or Scans tabs to change those settings. Or click OK to save all changes and return to the Assembly Options screen.

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