The reference directory contains the information for the reference that was used for aligning the data and/or detecting variants in sample. References are stored in their own folders in the references directory. SoftGenetics initially provides the necessary references files for your Geneticist Assistant installation. You use the Ref function that is available on the toolbar of the Geneticist Assistant main window to update to the most recent version of any reference in the reference directory. You can select multiple references for updating at the same time.