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Old 11-08-2013, 04:02 AM   #1
cindylanzao
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Default Ion Proton data analysis software

I am a newbie in this field, can anyone give me a list on the name of the current available software for Ion Proton data analysis?References recommendation is also welcome.Thank you guys so much!

Last edited by cindylanzao; 11-08-2013 at 04:03 AM. Reason: More complete
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Old 11-08-2013, 04:54 AM   #2
GenoMax
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If you are looking for the official Ion Torrent Suite software then as far as I know there is no way to get it unless you have a machine. (http://www.lifetechnologies.com/us/e...-software.html) There is a cloud version (but that is not free either: https://torrentsuite.lifetechnologies.com/)

Life Tech has the "Ion reporter software" that is cloud based. I am not sure if that is free but the information is available at the link above (look in the navigation bar on the left).

Otherwise the output from an Ion Proton machine is regular fastq-format data files. You can pretty much use any NGS software that can handle this data for analysis. One thing to keep in mind is the quality scores from Ion runs are not completely equivalent to normal phred scores.

Last edited by GenoMax; 11-08-2013 at 04:57 AM.
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Old 11-08-2013, 08:00 AM   #3
IonTorrent
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Hi there GenoMax,

In fact, Torrent Suite software (and a few other packages) is open source and is freely available via our github repository:
https://github.com/iontorrent

As mentioned on the Torrent Suite page, starting with our freely available virtual machine is another option. But these options are largely intended for developers, rather than people looking for an end user solution.

At the present time, Ion Reporter is available freely at the following location:
https://ionreporter.iontorrent.com/

The next version of Ion Reporter, which has a number of exciting updates and improvements, is due next month.

Quote:
Originally Posted by GenoMax View Post
If you are looking for the official Ion Torrent Suite software then as far as I know there is no way to get it unless you have a machine. (http://www.lifetechnologies.com/us/e...-software.html) There is a cloud version (but that is not free either: https://torrentsuite.lifetechnologies.com/)

Life Tech has the "Ion reporter software" that is cloud based. I am not sure if that is free but the information is available at the link above (look in the navigation bar on the left).

Otherwise the output from an Ion Proton machine is regular fastq-format data files. You can pretty much use any NGS software that can handle this data for analysis. One thing to keep in mind is the quality scores from Ion runs are not completely equivalent to normal phred scores.
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Old 11-08-2013, 08:11 AM   #4
GenoMax
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Thanks for those links. I will have to look into getting the software.

Curiously when this topic had come up locally no one from Life Tech said anything about the availability of the software on github (which was the origin of my comment above).

Is it possible to grab a folder of raw data from the proton/PGM and analyze it offline using a separate TS install?
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Old 11-08-2013, 01:17 PM   #5
IonTorrent
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Sorry, we might have missed the earlier post. Please do consider Ion Community for those kinds of requests as well - there are team members monitoring the various spaces who are dedicated to responding. We do value the great resource that SEQanswers is as well and try to respond where we can here as well!

Yes, that is correct. It is easiest starting from so-called WELLS files. The guidance in the Torrent Suite Administration Guide found on Ion Community should provide helpful information. Outside of that, the best course is to speak with a local Field Bioinformatics Scientist.


Quote:
Originally Posted by GenoMax View Post
Thanks for those links. I will have to look into getting the software.

Curiously when this topic had come up locally no one from Life Tech said anything about the availability of the software on github (which was the origin of my comment above).

Is it possible to grab a folder of raw data from the proton/PGM and analyze it offline using a separate TS install?
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Old 11-08-2013, 08:40 PM   #6
cindylanzao
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Smile Can someone offers me a guidance of Torrent suite?

I read the Readme, but I cannot find the guidance on how to use this software apart from the guidance of installing this software. Where can I get the manual? Thanks




Quote:
Originally Posted by IonTorrent View Post
Hi there GenoMax,

In fact, Torrent Suite software (and a few other packages) is open source and is freely available via our github repository:
https://github.com/iontorrent

As mentioned on the Torrent Suite page, starting with our freely available virtual machine is another option. But these options are largely intended for developers, rather than people looking for an end user solution.

At the present time, Ion Reporter is available freely at the following location:
https://ionreporter.iontorrent.com/

The next version of Ion Reporter, which has a number of exciting updates and improvements, is due next month.
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Old 11-10-2013, 03:45 AM   #7
GenoMax
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Quote:
Originally Posted by cindylanzao View Post
I read the Readme, but I cannot find the guidance on how to use this software apart from the guidance of installing this software. Where can I get the manual? Thanks
I think you can find those on the ion community site: http://ioncommunity.lifetechnologies.com/welcome You will have to become a member there.
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Old 11-10-2013, 03:55 PM   #8
cindylanzao
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Thanks to all you guys offering me help!
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