Entering edit mode
8.5 years ago
Augusta
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30
Hi!
I've just read a paper about the advantages and disadvantages of different NGS platforms. It says that the systems by Roche are faster than the Illumina systems but that the latter have a higher throughput. This revealed to me that I do not understand the definition of the term throughput correctly. I used to believe that the throughput is definied by the amount of data that is produced in a certain amount of time. So I would assume that the fastest technology is the one with the highest throughput. What is the difference, and how can a low-throughput method be quicker than a high-throughput technology?
Thank you in advance!
Your understanding is generally correct (though I don't think throughput is factored over unit time as you are thinking).
With certain non-illumina technologies (e.g. Ion proton, minION, PacBio) run times are relatively short (hours instead of days) so even though these technologies are faster (in terms of run-time) they are not as high-throughput (in terms of total amount of data) as compared to Illumina.
Possibly one may still get more data from an Illumina run (in terms of raw bases irrespective of the actual length of reads) if we did the run for the same length of time as say an Ion proton run (e.g. 2 hours). Disclaimer: This is just an illustrative example and the data produced may be very short and not usable.
Hi genomax2!
Thank you for the quick reply! If I want to sequence a whole human genome for instance, does that mean that a low-throughput technology will need more runs than a high-throughput technology, and might take longer in the end?
To achieve the same number of raw bases (ignoring Q-scores) .. yes. If you had access to multiple machines (e.g. ion proton) then then the time factor may not be longer. But in practice, you probably won't, so it may ultimately take an equal amount of time or longer.
We are not considering the cost factor at all so it is important to keep that in mind as well.
O.k. So is it in general advisable to choose a high-throughput technology for big amounts of data, and low-throughput technologies for smaller genomes etc? (Do you know why the throughput is so much lower for Roche technologies?) Thank you so much!
Basically differences in technology.
There are pro's and con's for every sequencing technology out there. So consider those (along with the cost, sorry to keep reminding you about that) before you make an informed decision about what technology to select for your application (that should count). Don't just go on quantity of data produced!
Don't worry, I won't! :-) I'm just trying to understand the background for now. Thank you so much (also John, although I don't know where your post went)! You spared me a lot of time and brainpower!
Take a look at this link. You will find it useful.
Yes, very useful!
By the time I hit post, Genomax had already said everything worth saying, so i deleted it to keep the signal to noise ratio up :)
Only thing i'd add now is that you might want to think about spending 10-20 minutes on YouTube checking out the promotional videos for all the different sequencing technologies out there, perhaps making short notes as you go. Although it is rather dull, particularly with the cheesy voice-overs, it's important to try and keep in mind how all this stuff actually works so you're more confident with what you know going forward.