GNomEx can accommodate dual index tags for Illumina HiSeq experiments. To take advantage of this feature, barcodes and barcode schemes must be configured in the Dictionary Editor.

First, a barcode scheme must be added. A barcode scheme is a grouping of barcodes that can all be used for the same protocol A barcode scheme can be added or edited in the dictionary manager under the 'Illumina Oligo Barcode Scheme' folder.

Once the scheme has been saved, barcodes can be added and associated with the appropriate scheme. Barcodes are added or edited in the 'Illumina Oligo Barcode' folder.

Now, the barcode scheme must be associated with a seq lib protocol. To do this, a new entry must be added to 'Illumina Oligo Barcode Schemes allowed Platforms'. When adding a new association between barcode schemes and platforms, a seq lib protocol is selected and then a barcode scheme is selected. If the barcodes in this barcode scheme are to be used as the second or B index for that protocol, the field 'Is Index Group B' should be saved as 'Yes'. For protocols that utilize dual index tagging, at least 2 'Illumina Barcode Schemes allowed Platforms' entries must be assigned. One should match the protocol with the barcode scheme to be used as the first index tag ('Is Index Group B' = 'No'). The other should match the protocol with the barcode scheme to be used as the second or B index tag ('Is Index Group B' = 'Yes').