Holding down the Ctrl key (in MacOS use ⌘Command key), select your file of trimmed reads and the reference sequence (yghJ CDS). Click Align/Assemble → Map to Reference, and reset to the default setting using the settings cog at the bottom left of the window.
Geneious will guess which of the sequences you have selected is the reference, but you can change this using the drop-down menu. In this case it has chosen correctly, and "yghJ CDS (divergent reference)" should be shown as the reference sequence.
Note that in Geneious 8.1 and above, the reference sequence does not have to be pre-selected before opening the Map to Reference window. Instead, it can be selected from any folder in your database by clicking the Choose button within the setup options.
In the Method panel, ensure Geneious is chosen as the Mapper. A number of different mapping algorithms are available here, and these have varying strengths and weaknesses depending on the type of data you are assembling. A brief outline of the different algorithms available is given here.
The Sensitivity should be set on Medium Sensitivity/Fast. Geneious will automatically choose an appropriate sensitivity based on the size of your dataset. For next-generation sequencing, Medium or Medium-Low sensitivity is recommended, as using High Sensitivity will take a long time and is unlikely to improve the results if you have sufficient coverage. The Fine Tuning option can improve the results by aligning reads to each other in addition to the reference sequence - set this on "Iterate up to 5 times".
Ensure Do not trim is selected, and under the Results panel, choose Save assembly report and Save contigs. Uncheck "Save in subfolder" if it is selected. Your Map to Reference options should now look like this:
Click OK to run the assembly - it may take a few minutes to complete.
Two new documents should now be created in your document table - a contig of the reads mapped to the reference, and an assembly report. Open the assembly report and you will see how many reads were assembled, how long it took, and what contigs were produced. We will explore the contig document further in the next exercise.