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

The table below shows editable options. 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
Mer size The minimum length of a mer (overlapping region of a fragment read), in bases, required to be considered a match when arranging reads into contigs. Mer size information is used to identify matches during the assembly layout phase. The default mer size is determined by the selected read technology and is shown in the window. For more information, see How mer tags are chosen.

  • Automatic – Select this button to automatically set the size based on assembly type and sequencing technology.

  • Custom – Select this button to choose the size yourself. You must enter the desired number of base pairs in the field at right. Lowering the mer size increases the sensitivity of finding matches, but also increases the likelihood of finding spurious matches in addition to the correct match. Lowering the mer size can also greatly increase the requirements for storing intermediate and temporary files with large projects. 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.
Mer search range The maximum distance upstream that the long read aligner will look for exact mer matches of the specified length. Distance is calculated in gapped coordinates. Enter thresholds for both the First pass and Second pass of the alignment phase.
Minimum depth percentage to confirm Enter thresholds for both the First pass and Second pass of the alignment phase.

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

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