Adapter/Quality Trimming and Filtering
BBDuk (decontamination using kmers) is a fast and accurate tool for trimming and filtering sequencing data that is part of the BBTools package by Brian Bushnell. The plugin makes it easy to trim adapters using presets for Illumina Truseq at the same time as trimming by quality and filtering out any reads that are trimmed to below a certain length.
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.