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The generation of sequencing technologies has come on leaps and bounds and there are stark differences between the types of technology used. There is a great Q&A here What is the difference between second and third generation sequencing?

NGS refers to high throughput massively parallel sequencing technology (See illumina's marketing page). 4th generation sequencing has been used to describe single molcule nanopore based technology (Nanopore-based Fourth-generation DNA Sequencing Technology).

So is NGS just a massively parallel version of 4th gen, or is there a more fundemental difference?

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I think that all of this is pure marketing and can be safely ignored. There is no basis for the generations of sequencing in chemistry or instrumentation, except possibly that second-generation (Illumina) was a massive parallelization of first-generation sequencing (Sanger) through clever chemistry and instrument modifications. It is merely "I want to argue that this technology occupies a particular niche right now".

All of these terms are obviously very imprecise. I had not heard "4th-generation" before; having analyzed all of these data types, I personally would lump nanopore into the third-generation sequencing box with PacBio: they are long, relatively noisy reads that grew popular around the same time for roughly the same applications and are currently under very active research and development.

I would allow that these two technologies (PacBio and nanopore) are definitely distinct from Sanger (much older, now fairly restricted to specific applications like confirming plasmid sequences) and Illumina (older, mature tech with deep market penetration, making tons of money and trying to hold onto market share).

"NGS" itself is a rather silly term for similar reasons, as it is now clearly a technology that is fighting for relevance in certain applications where it was once dominant (e.g. genome assembly). If we must apply generational terminology to Illumina, it is clearly second-generation. This is one of Joe Felsenstein's oft-repeated rants.

Nanopore itself is as far as I know established in 1996, whereas the first publication I am aware of that forms the basis for PacBio is 2003. For comparison, the Solexa sequencing that became the basis of Illumina instruments from thence was introduced in 2005. So any meaningful chronology also does not support these generations.

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    $\begingroup$ Illumina sequencing is not massively parallell Sanger sequencing. Sanger generates different length sequences each with a single labeled base. Illumina labels all the bases, takes an image, the strips the label off, and adds the next labeled base to image. $\endgroup$
    – swbarnes2
    Nov 1, 2021 at 16:07
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    $\begingroup$ @swbarnes2 that is a good point- I would still label the chemistry as derivative (sequencing-by-synthesis, but a lot, and with optics and fluorophores and non-terminal chain extension), but I will correct my answer. $\endgroup$ Nov 1, 2021 at 16:29
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    $\begingroup$ Nanopore took longer to commercialize though (by ONT, 2015) compared to SMRT (by PacBio, 2011). This adds massive confusion to any attempt to order these two. Some authors use LRS (long-read sequencing) to group them. There was also pyrosequencing, which has now been commercially discontinued, as another "generation" perhaps. $\endgroup$
    – Fizz
    Nov 3, 2021 at 9:31
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    $\begingroup$ There was a slightly more clear Q here about those (commercially speaking) pre-2010 "NGSes" biology.stackexchange.com/questions/7075/… $\endgroup$
    – Fizz
    Nov 3, 2021 at 9:55

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