Note: This topic is not applicable to BAM-based projects.
You may want to use a known sequence as a backbone upon which to build your sequence assembly. This can be useful if you know the sequence of a chromosomal region of an organism that is closely related to the one you are sequencing. You may be able to perform the assembly with lower average sequence coverage, thus saving a substantial amount of sequencing effort.
To use a full or partial sequence, do the following:
1) Start a new assembly project and add the sequence you want to use as a backbone, as well as the sequences in your dataset.
2) Select the backbone sequence in the Unassembled Sequences window by clicking on it.
3) Click the Mark Ref button.
4) If desired, click the Set Ends button to access the Set Ends dialog, enabling you to choose endpoints for your backbone sequence.
5) Select all sequences except the backbone sequence in the Unassembled Sequences window.
6) Click the Options button to access the Preassembly and Assembly Options dialog.
7) Choose your preassembly options and then click Scan Selections.
8) Click Assemble.
9) After assembly, select the backbone sequence from the lower pane of the Project Summary window.
10) Select Sequence > Unmark Ref.
11) Select Edit > Negate Weights to prevent the backbone sequence from contributing to the consensus. The negated sequence will now be displayed in the Alignment View in the color specified for Negated Weight Color in the Editing & Color parameters.
Note: To negate the weight of only a portion of the backbone sequence, first double click the name of the backbone sequence from the Project Summary window to open it in the Alignment View and highlight the desired portion.