it depends upon number of amplicon libraries and how do you want to do them, in single run or not

in general it varies for 1700$ per 100 amplicon libraries for single run

You asked two questions: Cost for metagenomic library, and cost for metagenomic analysis. If you meant library, a gross estimate would be about $50-$100 per sample if you do the DNA isolations yourself. But the real answer is: it depends on what you are trying to accomplish. Eukaryots in the sample will dominate the DNA sequence reads. If you can select or enrich for bacteria that might help, but most likely you'll need to do some sequencing runs to get empirical data on the number/amount of bacteria, and then determine how much coverage you'll need when using only the bacterial data from your mixed samples (i.e. throwing out the Euk data). The cost of sequencing those libraries varies a lot, but another gross estimate is $15 to $35 per billion-base-pairs. Once you have an estimate of bacteria present, and coverage needed, then figure the bp needed per experiment, and pick a sequencer that can fit your samples together if possible, to minimize technical variability.

Peter Hoyt Thank you for your thorough response and understanding of the processes. Apologies for asking two questions rather unclear. I now have a more focused picture of the discussion needed with my PI. Thank you again.

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best wishes