I have worked with 454, Illumina and Solid platforms commonly referred to as 2nd generation (or next gen) sequencing platforms. Has anyone here worked with the Helicos system?
What other novel sequencing methodology/technology do you know of?
In lieu of first hand experience we'll take hearsay as well.
Hi there,
There's a lot of new technologies just about to come to market. To name a few of the ones already with some benchmarks:
By definition, Heliscope is still a 2nd gen. It uses the same technology (very sensitive/fast with high resolution CCD and reaction/synthesis followed by light emission). There's no real science on Heliscope yet because it's quite expensive (~U$ 1M, just the equip). But, as RIKEN acquired four of them, I believe they're worth the try. Just to mention, anyone can follow high throughput tech on this clever assembled map.
PacBio, Nanopore and Ion Torrent are real 3rd gen. They use a completely different approach. And Ion Torrent is truly amazing !!!
There a lot of discussion about 3rd gen in SeqAnswers in topics about the AGBT meeting.
In my opinion, Polonator is the most overlooked one. Despite being 2nd gen, it's open hardware approach ensues the possibility of transforming it on a heliscope-like machine or in a ion torrent-like.
Just had a look at a pubmed search for "Helicos" (14 hits) . The idea of being able to sequence RNA directly is promising. However to me this seems more like big marketing fuzz than real science. I didn't find an independent publication using Helicos, seemingly at present only Helicos uses/can use Helicos, at least what I saw all the Nature papers were "tightly affiliated" to the company. If there is one independent, please put it here. This at least would qualify for 3rd generation, in the sense of "not ready yet".
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Is 3rd generation sequencing definable? What makes Helicos 3rd generation, and not 2nd generation? Is it the single molecule nature of the sequencing technology that does it?
I think what is changing the way we think is more in novel applications of fast sequencing methods: RNA-seq, ChIP-seq, methylation profiling or conformation detection (C3 seq). Found this for example: http://www.ncbi.nlm.nih.gov/pubmed/18703132.
New applications are made possible by increasing speed, while they increase the demands to speed, which allows for more novel apps and so on (very much alike CPU power).
It would be also great to comment on the robustness of the data coming from these technologies as they are still in their infancy -- compared to the 2nd gen. where robust pipelines are about to be developed.
Reportedly the Helicos technology does not rely on amplification during the sequencing process. That seems like a substantial improvement over existing methods where the signal can be artificially increased.
What I was after was technology that changes the way we interpret sequencing data. But it may be premature to expect another radical change like the one that current methods brought forth.