How to calculate sequencing depth for 16S amplicon sequencing

Question

[sifujio]

Hi all, I would like to know how can I can calculate sequencing depth for amplicon sequencing.

I am conducting a microbial survey sequencing 16S rRNA's V3-V4 region which yields an amplicon of ~450 pb. So for each sample I have a mixture of different amplicon size (around ~450pb) for each bacteria's 16S that got amplified with the primers I used.

I would like to use the The Lander / Waterman equation C=NL/G, but since I am not sequencing a whole genome but a set of unknown quantity of bacteria's 16S, I don't know what number to put in. I am actually not even sure if it's possible to calculate it, at least with that formula..

Please help

Cheers

Answer 1

[mikhail.shugay]

Read coverage and organism abundance will interfere in such setting. I would recommend to focus rather on sample diversity metrics (see http://www.pnas.org/content/108/Supplement_1/4516.full.pdf+html ).