Costs of Amplicon Sequencing Experiments?

I would like to sequence the V4 region of 16s rRNA and was hoping some QIIME2 users could tell me what they pay for this service? Or what the most cost-effective process is?

Ideally, I would like to submit clean DNA and let the sequencing facility take care of the PCR and library prep.

Thank you very much for your time and experience.

Hello Stephan,

We usually budget about $100 per sample. Smaller projects often cost more per sample, while bulk orders get a discount.

I would interested to learn what other teams pay!


PS. Illumina claims $18 per 16S sample on this page, but that’s just what it costs to do a MiSeq run.


I too am very interested in this topic and was recently calculating the cost for my own methods. Without a doubt it is most cost effective to make the library yourself and submit it to your institution’s sequencing core. But again, there are some up front investments so if you don’t plan on doing sequencing or amplicon sequencing often it probably does not make sense to make those purchases.

I am aware of people paying anywhere from 50-350 USD/sample for amplicon sequencing and there are a number of choices that can drastically affect the price including sequencing depth: I am aiming for 50,000 reads/sample. For the protocol I use with everything ‘at cost’ the per-sample consumables cost to get from frozen sample to fastq is about 15$/sample. That price doesn’t include HR and amortized equipment and service contracts (mostly the sequencer) which add a significant chunk and explain a lot of the discrepancies between the consumable cost and core prices.