Currently, we are about to begin developing RAD-seq libraries. We are following the single-digest protocol by Amores et al. 2011 (Amores, Angel, et al. "Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication." Genetics 188.4 (2011): 799-808.). Since, we are going to buy the P1 and P2 adapters, we thought it could be possible to use combinatorial indexing to reduce the number of oligos we need to buy, i. e., instead of buying 40 P1 adapters and a single P2, we reason we could buy 20 P1 adapters and two P2. We think that should help us reducing prices, without compromising samples demultiplexing by using the combinatorial indexing of both adapters. However, within our knowledge, the refereces we have seen following Amores et al. 2011 (or other related protocoles), never use combinatorial indexing. We have always seen this kind of indexing used on ddRAD. Is there a specific reason for this? Can combinatorial idexing be used on sdRAD? and if so, do you have P2 adapter sequences with indexes you could share with us to achieve this?