What guidelines should I follow when pooling indexes?
What guidelines should I follow when pooling indexes?
For HiSeq®/MiSeq® instruments, Illumina uses a red laser/LED to sequence bases A and C, and a green laser/LED to sequence bases G and T. For each cycle, both the red and green channel need to be read to ensure proper image registration (e.g., A or C and G or T must be in each cycle). If this color balance is not maintained, sequencing the index read could fail.
For NovaSeqTM, NextSeq®, and MiniSeqTM instruments that use two-color chemistry, valid index combinations must include some indexes that do not start with ‘GG' in the first two cycles.