I just recently answered a question on Quora about the number of “sequencing generations” there are. (My answer was basically that the concept of generations for sequencing has never been used consistently, doesn’t make much sense and isn’t very helpful.) In doing so I quickly categorized the various technologies based on a number of attributes:
1) sequencing-by-synthesis vs direct sequencing (vs ligation vs hybridization)
2) stepped vs continuous sequencing
3) optical vs non-optical detection
4) short vs long reads
5) single molecule vs amplified
And here’s how I mapped the major platforms to these categories:
Illumina = SBS, stepped, optical, short read, amplified
Ion = SBS, continuous, non-optical, short read, amplified
PacBio = SBS, continuous, optical, long read, single molecule
Oxford Nanopore = direct, continuous, non-optical, long read, single molecule
Helicos/SeqLL = SBS, stepped, optical, short read, single molecule
454 = SBS, continuous, optical, short*, amplified (* considered ‘long reads’ at the time, but now at least an order of magnitude shorter than the long read technologies)
SOLiD = ligation, stepped, optical, short read, amplified
I’d be curious to hear what others think. The least satisfying is the “stepped vs continuous” category. ONT doesn’t fit perfectly cleanly as they could be considered “stepped” since a ratcheting protein is used, but it doesn’t have the distinct cycles of Illumina’s SBS chemistry. Also, I wasn’t 100% sure about the Helicos technology – is it cycle driven or continuous like Ion? Thoughts?
1) sequencing-by-synthesis vs direct sequencing (vs ligation vs hybridization)
2) stepped vs continuous sequencing
3) optical vs non-optical detection
4) short vs long reads
5) single molecule vs amplified
And here’s how I mapped the major platforms to these categories:
Illumina = SBS, stepped, optical, short read, amplified
Ion = SBS, continuous, non-optical, short read, amplified
PacBio = SBS, continuous, optical, long read, single molecule
Oxford Nanopore = direct, continuous, non-optical, long read, single molecule
Helicos/SeqLL = SBS, stepped, optical, short read, single molecule
454 = SBS, continuous, optical, short*, amplified (* considered ‘long reads’ at the time, but now at least an order of magnitude shorter than the long read technologies)
SOLiD = ligation, stepped, optical, short read, amplified
I’d be curious to hear what others think. The least satisfying is the “stepped vs continuous” category. ONT doesn’t fit perfectly cleanly as they could be considered “stepped” since a ratcheting protein is used, but it doesn’t have the distinct cycles of Illumina’s SBS chemistry. Also, I wasn’t 100% sure about the Helicos technology – is it cycle driven or continuous like Ion? Thoughts?
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