Question: Suitability Of Ion Torrent For 16S Tag Sequencing?
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gravatar for Michael Barton
7.8 years ago by
Michael Barton1.8k
Akron, Ohio, United States
Michael Barton1.8k wrote:

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?

ADD COMMENTlink written 7.8 years ago by Michael Barton1.8k
1
gravatar for Jeremy Leipzig
7.8 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

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/

ADD COMMENTlink written 7.8 years ago by Jeremy Leipzig18k
1
gravatar for Daniel
7.7 years ago by
Daniel3.7k
Cardiff University
Daniel3.7k wrote:

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

ADD COMMENTlink written 7.7 years ago by Daniel3.7k
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