BBMap
Fast and sensitive aligner for RNA and DNA
Requires Geneious 9.0+
Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).
Once installed, run the plugin by selecting your reads and reference sequence then clicking on Align/Assemble - Map to Reference in the toolbar. BBMap is available as an option in the Algorithm drop-down menu.