Note that this task is for adding indexes for alignment to the whole genome. If you want to align to the transcriptome or another set of genomic features, see Adding Aligner Indexes Based on an Annotation Model.

Click the green plus () icon next to the Reference Files section header and choose Reference sequence from the Library type drop-down list in the Add reference sequence dialog (Figure 1). Alternatively, click the Add library file button and choose Reference sequence from the Library type drop-down list.