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Old 01-07-2015, 08:58 PM   #1
BioGenomics
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Location: Belgium

Join Date: Apr 2009
Posts: 24
Question 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 !!!
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