Where can I find the index sequences I need to enter into the sample sheet?

For the Lexogen UDI 12 nt Unique Dual Indexing system, all sequences are given in the Lexogen UDI 12 nt Unique Dual Index Sequences file, available here. Sets A and B already take the different read-out orientations of different Illumina instruments into account. The use of the "i5rc" index sequences is only required for the use of Set A UDIs on Illumina instruments using the Reverse Complement Workflow (and vice versa for Set B UDIs used for Forward Strand Workflow).

The i5 sequences for the 6 nt indexing system in both orientations are provided for download in the Lexogen i7 and i5 Index Sequences excel file, available here. Although indices are 6 nt long, please note that if you are running 8 cycle index reads, then the first 2 nucleotides from the adjacent adapter sequence need to be added to the sequence in the sample sheet. These are: AC for i5 (forward orientation), and GT for i5rc (reverse complement orientation).