Click the green plus () icon next to Reference aligner indexes section header on the library file management page. Alternatively, click the Add library file button, choose Aligner index from the Library type drop-down list and whole genome from the Index to drop-down list. If an aligner index is already associated with an assembly, it will not appear in the Aligner drop-down list. If all but one of the possible aligner indexes have been added, the remaining aligner index will be the only option and will not appear in a drop-down list (Figure 1).