I'm trying to sequence amplicons of the 16S V3-V4 region (aprox. 540 bp). I've read that at least you need 10,000 reads per sample to characterize a microbial community. If I'm expecting at least 20,000 reads per sample, how can I know how many samples can I sequence at the same time? Aside from the limit of barcodes. We are planning to use a 2 x 300 bp run. Thank you in advance.
Depends of what kind of microbial community do you want to study. I mean, for soil microbial communities it is better to have more sequences per samples, around 40.000 sequences, and in another less diverse ecosystems (water, vegetal tissues, intestinal microbiota...) is enough with 10-20K sequences per sample.
In another hand, for Miseq sequencing you will obtain around 10-15 millions of reads. In the worst scenario, you will have 10 millions, if you want to have around 20.000 sequences per read, it is better to estimate to have 40.000 reads per sample, because after filtering you are not going to have the same amount of reads per sample. 10 millions / 40.000 reads = 250 samples. If I don't remember bad, the limit of barcodes is something like 384.
Good luck!
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