Map to Reference is used when you wish to assemble sequences to a known sequence, for example to locate differences or SNPs. To perform assembly to a reference sequence select your sequences and click Align/Assemble and choose Map to Reference. Choose the name of the sequence you wish to use as the reference in the Reference Sequence chooser and click OK. One contig will be produced per reference and this will display the reference sequence at the top of the alignment view with all other sequences below it.
The options available in the Map to Reference setup dialog are similar to those for de novo assembly (see section 10.3 ), with a few differences detailed in the subsequent sections. In the Methods panel, you can choose between the standard Geneious assembler, Geneious for RNAseq (R9+), or the BBMap, Bowtie or Tophat mappers if you have these plugins installed.
See chapter 11 for details on identifying differences or SNPs in your assembly.