Difference between Ion torrent proton and Ion PGM

[Bionerd]

Dear all,

I am completely new to ion proton data. I've been reading papers that were discussing about Ion torrent (most of the times I did not find Ion proton), but I've been asked to analyse Ion proton data. I would like to know what are the differences between Ion proton and Ion torrent (and also Ion PGM. Are they same?). I don't want to use the variant caller that comes with the sequencer. Can I use the data analysis pipelines of Ion torrent to Ion proton data (Do I need to change parameters of tools any time?). What are the characteristics of Ion proton data (mean read length, qualities..etc), error profile of the Ion proton sequencer? Any help will be greatly appreciated.

Thank you.

[GenoMax]

Physically they are different instruments but they work on the same principal (semi-conductor sequencing, using measurement of change of pH after incorporation of nucleotides). Both instruments will produce data in standard sanger fastq format so you can use any data analysis pipeline. Ion technology is sensitive to homopolymer stretches (http://journals.plos.org/ploscompbio...l.pcbi.1003031).

[cmccabe]

Our lab has been using the PGM for over 2 years for panel sequencing. We are in the process of validating exome sequencing on the proton. In addition to what @GenoMax has said the amount of data that you get on the PGM is roughly 10x less than the proton.
For example, on a 316 chip we usually get about 3.5 million reads with a file size being about 3GB.
On a P1 chip we get about 30 million reads with a file size of about 18GB. I hope this helps.

[Bionerd]

@GenoMax: Thank you for your reply. The mentioned details in this paper are also applicable to Ion proton instrument? or Do they vary? Because the title itself is indicating PGM data. I'm a little confused.

[Bionerd]

@cmccabe: Thank you for your information. Can you please direct me to any source where I can get the data characteristics?

[cmccabe]

The ion community is a good place to get information (requires an account)

https://ioncommunity.thermofisher.com

There you can get a lot of useful and helpful information.

Here are a couple more:

https://www.thermofisher.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html

http://allseq.com/knowledgebank/sequencing-platforms/life-technologies-ion-torrent

[Bionerd]

@cmccabe: Thank you. I've seen those sites. I've posted in Ion community, but did not get any reply yet. So thinking for an alternative source.

[ajthomas]

Ion Torrent is the company/brand name. Ion Torrent's sequencers are the PGM and the Proton. Functionally they are very similar in that they use the same chemistry and principles. The primary differences are only in output and read length. The Proton produces much more data, but read lengths are less (~200 bp for Proton, ~400 bp for PGM). You should be able to use the same pipelines for data from either instrument with little to no alteration.