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Old 04-23-2012, 07:16 PM   #6
Shawn Baker
Location: San Diego

Join Date: Aug 2008
Posts: 84


I saw a similar question to this on LinkedIn, and this is what I posted:

Points to consider about the MiSeq:
• Good choice if you already have access to a HiSeq (either your own or through a collaborator) as the workflow is very similar and the libraries will be cross compatible.
• This is generally considered the easier/simpler of the two platforms.
• Read length and output per run has been expanding, but not at the rate for the Ion Torrent platforms
• Runs are relatively quick (~24 hours), but not nearly as quick as for Ion Torrent (2-4 hours)

Points to consider about Ion Torrent:
• The Ion Torrent PGM is the “lower throughput” machine which is topping out at ~1Gb per run (much less than the MiSeq)
• The Ion Proton is the newer instrument which should have outputs of 10Gb (sometime this summer) and 100Gb (by early next year) – 100Gb is substantially more output than what Illumina has said the MiSeq will be capable of producing.
• The Ion Torrent machines have substantially quicker runtimes (~2-4 hours vs ~24 hours)
• Currently, both the PGM and the Proton use emulsion PCR for amplifying libraries prior to sequencing. While there are kits and instruments to help automate this, emulsion PCR is generally considered to be more of a hassle than the ‘bridge amplification’ that the MiSeq uses .

Feel free to check out BlueSEQ’s knowledge bank for more in depth, neutral assessments of the various sequencing platforms:

Also definitely check out Nick Loman's paper.

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