Suitability Of Ion Torrent For 16S Tag Sequencing?

Question

[Michael Barton]

The advantages of the Ion Torrent (IT) for 16S tag sequencing are a relative cheap machine with a relative cheap cost-per-run. I wonder if an IT has the necessary read length and fidelity. I have read that the mean read length of an Ion Torrent 318 can be above 200bp. Furthermore 454 data, which I believe has a similar error structure to an Ion Torrent, can be used for community analysis albeit perhaps not for phylogenetic tree construction.

Has anyone tried using using an IT for this? Could IT be used for this application?

Answer 1

[Jeremy Leipzig]

16S was part of the proposal presented by Mitchell Sogin which won him a free machine.

http://www.iontorrent.com/videos-ion-pgm-gordon-moore-environment-grant/

Answer 2

[Daniel]

I would personally be very sceptical of assigning taxonomy to such short reads given the resolution that you would receive, but it can be done: (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2566877/)

Also, read quality can be a problem with diversity analysis (ie 454 and AmplicoNoise). This is interesting regarding IT: http://www.edgebio.com/blog/?p=271

I'd still be very interested to see how it works out. I think their current objective is to double read length in 12 months which would definitely put it in the realm of amplicon sequencing, so I think only time will tell