Hi all
Currently we are sequencing 16s amplicons on our MiSeq using the Caprasso primers. I have people asking to do a variety of non-16s amplicons and will likely use a 2step PCR approach to minimize the primer costs. So now I'm trying to decide if we should use the nextera index kits (costly) or make our own primers (probably based on the dual index 16S primers from the Schloss lab).
Other than the cost, what should I consider to compare these two approaches? I plan on using Phusion polymerase in both steps if using the homebrew index approach.
thanks
Currently we are sequencing 16s amplicons on our MiSeq using the Caprasso primers. I have people asking to do a variety of non-16s amplicons and will likely use a 2step PCR approach to minimize the primer costs. So now I'm trying to decide if we should use the nextera index kits (costly) or make our own primers (probably based on the dual index 16S primers from the Schloss lab).
Other than the cost, what should I consider to compare these two approaches? I plan on using Phusion polymerase in both steps if using the homebrew index approach.
thanks
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