You can use 12 bp UDI sequences on MiSeq systems, but due to the limitations of the MiSeq Kit chemistry, the following adjustments are required:
- Read both index sequences at their full 12 bp length, but reduce the length of Read 1 and Read 2 by two bases, resulting in a 2x299 bp read for the 300-cycle kit.
- Alternatively, you can read the index sequences at 10 bp each. However, for some of our UDIs, this may result in an edit distance of 2. In such cases, ensure that demultiplexing is performed using only perfect index matches (mismatch = 0).