“It’s a lot cheaper to buy PGM compared to other sequencing platform. So, should we buy it?”
A common concern regarding this question is whether the sequencing quality is alright? This is one of the first concern Ion Torrent seems to have experience since they first launched their first sequencer.
Quail, et al took a look at three platform in their paper. Although they have only looked at microbial genome with variable GC/AT content. They showed that there still seems to be a problem with Ion Torrent PGM platform when they sequence Plasmodium genome. Moreover, the false positive rate of base calling from Ion Torrent platform is still higher.
This data may not be applicable to human genome sequencing, but it deserves a closer look in my opinion.