Hello, Qiimers,
I would like some advice on my sequencing protocol. I normally use V1-V2 for my 16S sequencing; however, I plan to go V3-V4, as per the standard Illumina protocol for my next project. For what I understand, I should expect a ~460nt PCR product. I was wondering if sequencing 250x2 would be sufficient (40 nt reads overlap), or if you would rather suggest going 300x2 (140nt overlap). The former seems sufficient in my opinion, but it is the first time I use this region, and I would like to hear your opinion.
Best,
Max