Excuse me:
How shou'd I understand the concept of throughput? Does it mean the length of read or the output data amount or the speed of bases platform produces? I am very confused.
Any help that gave me a light would be much appreciated.
Many thanks in advance!
It's the amount of data. Previously, Sanger sequencing was used where you would load a 96 or 384-well plate into a machine and get that many sequences out. While the results were extremely good quality (for the most part), this isn't a very effect way to sequence a whole genome (or transcriptome, or anything else for that matter), since the sequences only got to 800bp or so (1kb if you were super lucky). NGS totally changed that, now that we can sequence a whole human genome at 30x coverage in a single run of one machine.
BTW, it's only recently that the length of NGS has really caught up to (and now surpassed) that of the older Sanger method. Also, the original term for NGS was MPSS: massively parallel short-read sequencing (or something like that), where the "throughput" concept is a bit more obvious.
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Also, High Throughput Sequencing (speaking of glaringly obvious names). Shouldn't we now start calling Next-gen Current-gen? ;)
Looks like we should. I've been asked several times by reviewers to change NGS -> HTS throughout the paper for exactly this issue :)
Talk about minor change! Do they complain about American vs. British English spelling as well or take firm positions on the oxford comma?
some journals/reviewers certainly do
Yeah, some people are now talking about 2nd, 3rd, etc. gen sequencing. My understanding is that Illumina is considered 2nd gen (I assume Sanger would be 1st gen and the old "gel slab" method would then be 0th gen :P ). I've seen single molecule stuff referred to as 3rd gen.
We are so desperately in need of standards!