How many reads are needed?

Theory behind mothur
1

Hi,

I am trying to keep our costs down as a sequencing core so I’m trying to determine how many reads per sample are needed for 16S identification? I realize that this will be dependent on the complexity of the microbiome but I feel like we get more reads than we actually need by multiplexing 384 samples on a 500 cycle v2 MiSeq run. Input is much appreciated, my users will be happier if I can keep the sequencing affordable!

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constantly open question. we learned quite a bit about microbial communities when we were looking at <100 clones/sample pre-NGS days. I think 5000-10000 is pretty reasonable and will question users who want more (clarifying that I’m willing to do it and charge them for it, but that in general I think it’s unnecessary)