Best alternative for Nextera Indices for multiple amplicon resequencing experiment ?
Hi all,
after using the 96 plex double indexing kit (8 X 12 indices) of Illumina for 16s studies, we now apply this for other amplicon resequencing purposes. But as expected this is a quite costly option and I would be interested to know of the best and cost-efficient alternative technologies for highly multiplex amplicon resequencing (50 inds X 12 amplicons for instance) or a list of 384 indices for instance to allow the 2-PCR step (amplicon + adaptor followed by indexing PCR with complementary tail to adaptor) to run on Miseq/HiSeq. I heard the Nextera adaptors had higher efficiency due to nucleotide alterations, so trying to reduce read nr variation /BC as much as possible. Our amplicons have been first BS converted, so we're looking at PCR sizes of 500 bp max for the MiSeq.
Thanks for your insights !!!
after using the 96 plex double indexing kit (8 X 12 indices) of Illumina for 16s studies, we now apply this for other amplicon resequencing purposes. But as expected this is a quite costly option and I would be interested to know of the best and cost-efficient alternative technologies for highly multiplex amplicon resequencing (50 inds X 12 amplicons for instance) or a list of 384 indices for instance to allow the 2-PCR step (amplicon + adaptor followed by indexing PCR with complementary tail to adaptor) to run on Miseq/HiSeq. I heard the Nextera adaptors had higher efficiency due to nucleotide alterations, so trying to reduce read nr variation /BC as much as possible. Our amplicons have been first BS converted, so we're looking at PCR sizes of 500 bp max for the MiSeq.
Thanks for your insights !!!