A Window Into Bioinformatics - Sequencing Costs

Consider the following scenario: your research lab has been around for a few years, and you are wondering whether all these sequencing services you are paying for are worth it - should you invest in buying your own medium-scale DNA sequencer?

Prelude - Nanopore Sequencing

Disclaimer: I am a fan of Oxford Nanopore Technologies (ONT). ONT has produced a sequencer that can do something no other commercial sequencing company can do: carry out [relatively] model-free discovery of novel polymers (e.g. DNA & RNA with modifications). Combined with their relatively public disclosure of information (especially with regards to pricing), I've been willing to work around numerous technical and operational issues because their "move fast, release early" philosophy works well with my preferred way of doing research.

If you're just starting out, don't have much money, or just want a taste of sequencing, then there's only one realistic option for an in-house sequencer: Oxford Nanopore's MinION. A MinION Mk1b Starter Pack with a 24-sample Rapid Barcoding Kit is available from Oxford Nanopore for $2,000 USD ($3,300 NZD). For another $1,460 USD ($2,400 NZD), you can get a Flongle adapter.

The Flongle adapter gives you access to Flongle flow cells, which are the cheapest per-run sequencing flow cells available at $810 USD ($1,350 NZD) for a pack of 12. Depending on the use case, the per-sample consumable cost can be quite low on Flongle, down to $8.50 NZD per sample when running 24 samples using the Rapid Barcoding Kit (which is competitive vs Sanger sequencing for anything more than a couple of 1kb reads per sample).

But this post isn't about MinION sequencing (a device that has a yield of 5-15GB for MinION flow cells, and 0.2-1 GB for Flongle flow cells); it's about sequencing on a device that can realistically and comfortably sequence a human genome in a single run.

Aside - GrinGene Bioinformatics

I (David Eccles) am the owner/operator of a sole-trader business - GrinGene Bioinformatics - and can provide more specific advice about high-throughput sequencing projects, from sequencing library preparation through to downstream data analysis and result presentation.

If you'd like to see more posts like this, please let me know in the comments.

If you have a research project that you'd like help with, feel free to contact me for advice. See here for more details:

https://www.gringene.org/services.html

Cost Summary

There are three popular players in the low-end large-scale sequencing market: Illumina, Pacific Biosciences (PacBio), and Oxford Nanopore (ONT). Here is an approximate breakdown of the direct costs to get a human-genome-scale system up and running from each company (costs are approximate, mostly based on conversion from USD to NZD, and don't include additional external costs):

Illumina NextSeq 1000

• Initial system capital cost: $350,000
• Cost per run: $7,400 (P2, 600 cycle, 400M read kit)
• Maintenance: $35,000 / year (estimate, assuming 10% of system cost)
• Yield per run (using the above kit): 240 GB
• Marginal kit cost per GB: $31
• Read length: 600bp
• Read accuracy: Q30 (99.9%)
• Sequencing run time: 34 hours

PacBio Revio

• Initial system capital cost: $1,300,000
• Cost per run: $1,650
• Maintenance: $75,000 / year (estimate, based on reported Sequel maintenance costs)
• Yield per run: 90 GB
• Marginal kit cost per GB: $18
• Read length: up to 20 kb
• Read accuracy: Q33 (99.95%)
• Sequencing run time: 24 hours

ONT P2 Solo

• Initial system capital cost: $38,000 (CapEx version)
• Cost per run: $1,650
• Maintenance: $1,650 / year
• Yield per run: 50-150 GB
• Marginal kit cost per GB: $11-$33
• Read length: up to 2 Mb
• Read accuracy: Q28 (99.8%)
• Sequencing run time: 5 mins to 72 hours

Capital Cost Recovery

From my perspective, the marginal per-run costs for the platforms are similar. In other words, a service centre with good cost recovery for capital expenses and maintenance could choose any one of these systems and get similarly cheap throughput.

However, most research labs are not service centres, so the maintenance and capital costs should dominate purchasing decisions. Here are the approximate maintenance costs taken from the above summaries:

• Illumina NextSeq 1000: $35,000 / year
• PacBio Revio: $75,000 / year
• P2 Solo: $1,650 / year

Assuming none of the sequencing runs were done internally, with a doubling of service cost to other people, here are the approximate number of gigabases required to sequence in order to recover the ongoing maintenance cost (and number of flow cells required):

• Illumina NextSeq 1000 (P2, 600 Cycles): 2300 Gb (10 flow cells / runs)
• Nanopore P2 Solo (PromethION): 100 - 300 Gb (2 flow cells; 1-2 runs)
• PacBio Revio: 8200 Gb (91 flow cells; 23-91 runs)

On the flip side, this is the minimum number of sequencing runs that would need to get done externally (with overheads being 50% of the service charge) over the course of a year as a service before it would make financial sense to consider buying one of these sequencers for internal use.

Given that the service market for sequencing is somewhat competitive, that 50% service charge assumption may be invalid. If the service charge were similar to (or lower than) the in-house reagent cost (which happens for Illumina sequencing due to steep volume discounting), it may not be possible to charge substantially more than reagent costs and still get sufficient demand for cost recovery.

Summary

For small volume sequencing (less than one sequencing run per month), a purchase of the Nanopore P2 Solo makes financial sense, as recovery of maintenance costs happens quickly. Due to the high maintenance cost of PacBio Revio, it doesn't appear to make financial sense as a purchase for a small lab in Aotearoa at any scale.

There are some nuances depending on application, but my general recommendation is the following:

• If you only want to do short-read sequencing (under 1000bp), then don't buy a sequencer; just continue to get sequencing done as a service from an established large-scale sequencing centre.
• If you want to do long-read sequencing (or a mix of short-read and long-read sequencing), then consider getting a P2 Solo. The ongoing maintenance costs are low enough that it can sit idle for almost the entire year and still be a financially-viable tool for discovery.

[header image: Illumina HiscanSQ and ABI SOLiD 4 sequencers at the Max-Planck-Institut für molekulare Biomedizin, Germany; stitched image from photos taken by David Eccles in 2011]