I would like to buy a next generation DNA sequencer. Any suggestion for a brand that can offer the followings 1. direct sequencing, no PCR needed 2. durable machine, less maintenance cost, 3. Lower running cost...
Outsourcing your next-gen sequencing needs will always be cheaper and less stressful...
Outsourcing your next-gen sequencing needs will always be cheaper and less stressful...
Illumina sequencer is better. Best way apart from this is outsourcing.
Thanks everybody, we are planning to set up a business of sequencing. So outsourcing can not be an option. It is apparent that all the next gen's are expensive. But which one will be of low running costs/low maintenance cost etc. This machine would work in southeast Asian country, so that's another headache to get technical support there as soon as it would be needed.
It depends on the customer profile and how large business you are planning. if you will just make exome seq for clinical purpose, Illumina miseq or nextseq may be enough. If you will also give sequencing services for de novo sequencing projects Hiseq 2500 also PacBio may be better. You should also mind how many samples are you expecting per day/week. I know several companies that bought hiseq 2000, but do not profit because of the inadequate samples.
If everybody has forgot it, I want to remind you, that the gold standard in DNA sequencing is ABI3700. If your sequencing amount is not that large, may be an ABI3700 is enough to start your business going, like sequencing a few genes, from a few species, or patients.
The next cheapest thing would be going to MiSEQ of Illumina. Its read length is ~100bp vs. ABI3700 1000bp, but has much higher density.
Thanks everybody. Dr.Tom Tang, I like your argument. But is it correct that Next gen sequence offers 99% accuracy in reading, while I know that in Shanger sequencing, ambiguity can cause problem if the DNA is not of high quality. Amount of DNA could be another concern-don't you think?
Arman:
I am not aware any difference in DNA amount requirement between Sanger and Illumina sequencers. If your DNA amount is not sufficient, PCR can increase the amount of DNA before you put them into a sequencing machine. But PCR is known to cause its own problem, like introducing bios against GC-rich sequences.
The only sequencer where DNA amount is not a matter is PacBio, at least theoretically. It requires a single copy of your template. This is the absolute limit. But PacBio only has 85% accuracy on any specific position, so to get Q30, you need 5-10 copies of the same thing. Of course 5-10 copies is a very low amount. So usually you don't need to do any PCR.
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