Long amplicons sequencing with Miseq

[pfeutry]

Hi all,

We're about to buy the nextera XT kit for 96 samples in order to sequence mitochondrial genome.

Our proposed strategy is:

-> Amplification of whole genome in 4 fragments (4-5kb each fragment) which are pooled for each individual.
-> Library prep with Nextera and sequencing of 96 samples in one Miseq run

Is there something we missed or should be concern with (problem with long range amplicon? non uniform coverage across regions or across samples? etc).

Thanks for your help.
Pierre

[Bucky]

Sounds good. Just make sure that you have a little bit of overlap between your amplicons (~300bp) since the tagmentation is not as efficient at the 5' and 3'

[pfeutry]

Thanks for this advice Bucky, anyone else before I go ahead?