What are the best barcoding - multiplexing strategies?

Hi @mshenton,

The EMP protocols are very commonly used for 16S V4:

Commonly used translates to fewer bumps down the road in figuring out protocols and analysis — so I'd recommend this as a tried and true method.

That said, some other schemes like dual-indexing can help decrease sequencing error slightly, but these come at greater expense since all primers are barcoded. I am hesitant to endorse any particular method without having tried them all.

There is a wide range of different methods used out there and surely an equally wide range of opinions — let's see if others on this forum have any opinions (and especially literature benchmarking different methods).

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