Reads coverage per sample

What is the recommended coverage depth for sequencing V4 or V3-V4 regions (stool samples) ?
100 000 reads?
10 000 reads?


Whatever you can get. Frankly, we put too much emphasis on read depth. We should be sequencing more samples to get more replication. 10 years ago people could get Science papers sequencing hundreds of sequences per sample :). I would also strongly advise against using V3-V4. See

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well, but certainly it should be more than 100 reads no? also more than 1000? 5000 is still to low?

We’ve published a paper with 800 (?) reads per sample. More typically it’s about 3000-10000. Generally, if you do a full MiSeq run spread over 384 “evenly” abundant samples you’ll be in good shape.

Hear hear, completely agree with Pat. I would always go with more samples than more reads per sample.

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