Sequencing depth and paired end reads length of 16s RNA metagenomics on water samples looking for low abundance organisms?

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Sonja Wende

if its really only ~15 organisms, you don't need much, probably even a few 100 reads would do. But that depends also on how different you expect their abundances to be. The read length depends on the length of the region want to sequences. If you want to merge pairs they need sufficient overlap (> 10bp)

Estelle Caine

Thanks for your reply :) I'm looking to find the low abundance organisms!