1. Running Time per run
- MiSeq : 4 hours (1x35), 19 hours (2x100), 27 hours (2x150)
- GS Junior : 9 hours
3. Cost
- PGM : 78k€ and 820€ (316 and 318 chip) for the cost per run
- MiSeq : 105k€ and 600€ for the cost per run
- GS Junior : 120k€ and 1000€ for the cost per run
4. Read length ?
- MiSeq : 680Mb (2X100), 1Gb (2X150)
- GS Junior : 1Gb, 500bp max by amplicon
I think each of this technology meets specific needs. I think you should also take into account : required quantity of DNA, automatisation cost (oneTouch, Fluidigm), technical support, availability (machine and kits), how old the machine is (GS Junior is the older one so its protocol is pretty stable), and how proven the technology is.
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