High Throughput NGS Systems: Throughput, Time and Cost Graphic

Authored by Dale Yuzuki on September 29, 2023

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It is an exciting time for next-generation sequencing (NGS) with new platforms being launched. Below is a chart that illustrates recent progress.

High Throughput NGS Systems compared by Gb/run, Days Required and $ per Gb
High Throughput NGS Systems compared by Gb/run, Days Required and dollars per Gb

A chart from 7 years ago…

A few days ago I was reminded of a chart from 2016, when a blogger named Lex Nederbragt (now at the University of Oslo, Norway) as a result of competition in the NGS marketplace for both readlength and throughput made a handy chart with a lot of platforms on it. (You can see his original blog post with links to the image in a post called “Developments in high throughput sequencing – July 2016 edition“.)

I was hopeful that that chart would have been updated in the intervening years, but alas his blogging moved platforms and then went quiet a year or so later. (And as a blogger myself, I can relate to the pressures of work and life as well as affiliation, which may or may not be conducive to this kind of activity.)

The current NGS “arms race”

So I thought about the current “arms race” of new platforms in the wings (i.e. Ultima Genomics is the top sponsor in February 2024’s Advances in Genome Biology and Technology), as well as new platforms only now getting into the hands of customers (specifically the Pacific Biosciences’ Revio, Element Biosciences’ AVITI, Singular Genomics’ G4, and the Pacific Biosciences’ Onso), and the renewed efforts of BGI / MGI / Complete Genomics now that they have the ability to sell their systems in North America and Europe. However complicating the MGI / Complete Genomics story, about a year ago parent company BGI Genomics was added to the US Department of Defense list of blacklisted companies – a GenomeWeb story with more details here, however as far as I can tell MGI / Complete Genomics continues to do business in the US.

By pulling together specifications and prices (along with some handy source materials assembled by others) I constructed a list of some 21 existing (or in the case of Ultima soon to exist) offerings for sale, from Illumina’s iSeq all the way up to MGI’s monster DNBSEQ-T20x2. I took this list, calculated a US Dollar per Gigabase cost based on the highest throughput x readlength x time to sequence, and excluded all the other configurations. (For example, using a lower number of flowcells, or shorter runtimes for tag-counting applications were excluded.) I also noted the number of hours it took for this highest-throughput-per-system calculation.

I then excluded all systems whose price-per-Gigabase of sequence was greater than $10 per Gb. (For those curious, if you figure 100 Gb of sequence per genome as a 33x WGS coverage, that’s the “$1000 Genome”). Therefore any system above the magic “$1,000 Genome” mark is not included, and you have the chart above: Gigabases per run on the X-axis, Hours per run on the Y-axis, and the size of the bubble in terms of US Dollars per Gigabase is relative to each other; the smaller the bubble, the lower the per-Gb cost.

A few observations

The market leader (estimated market share is about 75%) is of course Illumina, going through an upgrade cycle on the NovaSeq X where the per-Gb price on the NovaSeq 6000 at $4.84 drops to $3.20 in the latest iteration of the flowcell (these were released in February 2023, the 10B). A newer one (25B) will further drop that per-Gb price to $2.00 or so in the latter half of this year.

Element Biosciences has a ‘package deal’ to get to $2.00 per-Gb, however that’s dependent on special discounting and large purchase commitment; I’ve left it at their current maximum capacity use-case.

The Pacific Biosciences’ Revio did not make the cut due to higher than $10/Gb cost (from the pricing I’ve seen it’s about double that), but the Oxford Nanopore PromethION made it at exactly $10/Gb. Pretty remarkable that you can get a long-read whole genome for $1,000 when you think about it, even if it takes several days to produce the data.

The MGI / Complete Genomics systems are certainly price-competitive – and the DNBSEQ-T20x2 broke the chart at 72,000 Gigabases per run, at $0.99 per Gb. Yes, that’s 720 whole genomes at 33x every 4 days. Their other system, the T7, has a few installations worldwide when they were effectively blocked from selling them in North America and Europe due to patent infringement (and an injunction).

For the new Ultima system (called the UG 100), it has a relatively short runtime (24 h), a very low per-Gb price at $1.00, and at 3,000 Gb/run that is 30 whole genomes a day. Certainly a platform to watch, especially with the November 2023 ASHG conference coming up next month (in Washington DC) and the February 2024 AGBT conference (in Florida).

I will be attending ASHG this year, and if you’d like to meet in-person during that conference be sure to reach out!

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