Having worked with both platforms, in the wetlab (a few times) and especially with the data from both, I find Illumina to be the better far system for almost all applications.

Case in point:While our MiSeq is nowadays usually completely booked weeks in advance, the IonTorrent sits idle most of the time.

I have practical experience with Illumina MiSeq  and in my views its is better option. 

http://www.nature.com/nbt/journal/v30/n5/pdf/nbt.2198.pdf 

My team uses an Illumina MiSeq for targeted amplicon sequencing of cancer samples and it's been great. Sorry, no experience with Ion Torrent. This review from the Sanger Institute found more variants using Ion Torrent data, but with a higher rate of false positives: http://www.biomedcentral.com/1471-2164/13/341

Seriously Illumina MiSeq. You will probably have a better dept sequencing. However, I believe it is more expensive.

We've used both systems.  Illumina is the better choice - higher throughput and more accurate sequence.

I thank you all for your help. I find truly useful for the discussion that we have in our Department about which is the best choice to buy. I'm agree with you.

Regards,

Ginés

Having worked with both platforms, in the wetlab (a few times) and especially with the data from both, I find Illumina to be the better far system for almost all applications.

Case in point:While our MiSeq is nowadays usually completely booked weeks in advance, the IonTorrent sits idle most of the time.

Christian, thanks for sharing your experience with us. 

Have worked with both (although not recently w/the PGM) and would definitely advise Miseq over PGM. Even if the quality of the data were the same, the Miseq is far simpler to operate. 

Thanks Hilary for your help. We find it very useful.

I did not work with both of them but I received training on both of them in order to choose the best for our department, after careful study we discovered that Ion Torrent PGM , is the best.

PGM is following more accurate technology based on pH changes, while Miseq is based on the classical ccd method, so it can confuse the number of an array of Gs for example.

The software of PGM is powerful

The running conditions and the surrounding environment affects vey much the results of MiSeq but it doesn't with PGM

PGM is faster

PGM running cost is cheaper than Miseq

Thank you for your help, Samer.

PGM has faster runnings, notwithstanding, it need previous manipulation steps by operators, and therefore it may be subject to more manipulation errors.

We found that MiSeq running cost is cheaper than PGM if it is fully occupied.

Technology based on pH changes seems to be more accurate than the chemical method used by MiSeq, that is true. But PGM has problems with homopolymers (even with improved versions of their chips), for example.

If we look at bibliography, personal opinions of people with work experience with both platforms, and number of publications per platform in 2014, MiSeq seems to be the best choice for buying.

I had experience only with PGM Ion, but some colleagues in the field work with MiSeq. PGM is a bit more friendly to be handled than MiSeq. In another hand, I had many issues related to false negative InDels detected in the variant calling obtained from PGM data. This is suppose to be a problem of the Ion technology accordingly Ion users.

Hi Diego, are you saying you have more of the false negative issues? As previous comment from Catriona, review from the Sanger Institute mentioned PGM got false positive issue...

If you are going to use Ion PGM for 16s rRNA sequencing, I would recommend Illumina MiSeq over Ion PGM. I have done sequencing using Ion PGM and I found it very hard when it came to analysis. Ion PGM has in-built analysis platform which is Ion Reporter but it is not quiet in depth in my opinion. In fact 16 metagenomic kit amplifies 7 out of 9 variable regions which is great but because of that you have to modify Qiime analysis. I personally prefer illumina data as it gives you more independence in analysing data using Qiime in steps like quality control and selecting seq depth etc.

Please tell me you got a MiSeq over an Ion PGM.

Clearly MiSeq is the gold standard for 16S rRNA.

http://aem.asm.org/content/80/24/7583

Is there a reference for QIAGEN GeneReader NGS platform about its quality...