Hello Guys!

I`d like to know if there is a protocol that can suggest me to adapt my SNPs amplicon sequencing library and migrate from MIseq platform to a NextSeq one.

My protocol now consists in the usage of Read1 and Read2 illumina adapters plus two indexes (the plate-specific i7 and the well-specific i5). I add to the read1 and read2 adapters, a set of custom-designed primer sequences that will target the genomic regions where each SNPs I want to use is in. With this protocol I can target hundreds of SNPs and multiplexing hundreds of individuals in a single MIseq run. Soon, I need to migrate to a Nextseq sequencer and this kind of protocol (that works perfectly for a Miseq) will not match with the chemistry of a NextSeq sequencer.....I wonder if any of you have already experience running custom made genome-wide amplicon SNPs sequencing libraries that are compatible with a NextSeq platform?

Thanks a lot in advance for the help!!

Cheers

Paolo