There are two main ways to barcode WGS libraries so that they can be run together on a same lane:
– In-line barcodes: unique sequences are located at the very end of one or both adapters. This sequence will be at the very beginning of each read from a given library. This is the barcode system that is normally used fro GBS libraries as well.
– Indices: barcodes are in the middle of one or both adapters. These barcodes are read through an independent round of sequencing. For a paired-end library you would have therefore two rounds of sequencing of your fragment and a third round of sequencing for the index (and I guess a fourth one as well, if you have double indices). This is the system used in most commercial kits.