BBDuk
Adapter/Quality Trimming and Filtering
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 a sequence list of reads and choosing Annotate & Predict - Trim Using BBDuk... from the menu.