To import an entire folder and all its subfolders and ﬁles into Geneious Prime in one step, use the option File → Import → From Directory.... If the folder has subfolders, the folder structure will be retained when it is imported into Geneious. In version 10.1 and above zip ﬁles containing multiple ﬁles and subfolders can also be imported.
In version 11.1 onwards, Geneious supports bulk import of a mixture of SAM, BAM, GFF, BED, VCF and Fasta formatted ﬁles, allowing sequence, annotation and assembly information to be imported in a single step. Any combination of these ﬁles can be selected and then dragged and dropped into Geneious. The reference sequence will be loaded ﬁrst, followed by the annotation and assembly ﬁles. Sequence IDs in the ﬁles must match for the import to proceed correctly. If no reference sequence is present in the imported documents, you will be prompted to select a reference from existing documents in your database, or load onto a blank sequence.