V4 primers and Illumina adapters

Hi Mothur team,

I was hoping you could help. I was hoping to sequence the V4 region (primers 515F - 806R) of my bacterial communities. I have read how you recommend the Illumina MiSeq v2 2x250 kit.

However, if I were to use the Illumina adapters for sequencing would I have to use the v3 kit?

Have you any experience sequencing the V4 region with illumina adapters instead of your custom adapters?


Hi Ele,

We’ve tried with the v3 chemistry and it sucks for the V4 region (Why do I have such a large distance matrix). The main problem: if you do 2x300 the reads will go beyond the end of the fragment. We find that after 500 total base calls the quality crashes out. When we knocked the v3 chemistry back to 2x500 and reduced the cluster density to reduce the error rate, we basically got a very expensive version of the v2 chemistry. I’d stick with the v2 chemistry.