Ion Torrent PGM Analysis Pipeline

byou678 · 10-11-2012, 02:07 PM

Hi Everyone,

If anyone has Ion Torrent PGM data analysis experience here, could you please share your general/standard Analysis Pipeline? Thanks for any response!!

In addition, what kind of software do you mostly use?
Our department typically uses Partek and Galaxy. Any other recommended software based on your Pipeline?

ECO · 10-11-2012, 02:54 PM

Don't crosspost. Deleted your other thread. Thanks!

byou678 · 10-12-2012, 07:04 AM

Done. Thanks.

Could anyone give me some ideas? I really appreciate it!

Quote:

Originally Posted by ECO

Don't crosspost. Deleted your other thread. Thanks!

arolfe · 10-12-2012, 09:18 AM

Mostly you can use whatever tools you'd use for data from another platform. The PGM gives you a FASTQ or SFF file that you can pass to your favorite mapping/assembly/whatever program.

There are some Ion Torrent specific or adapted tools that
1) may provide better results because they've been tuned for the PGM's error model
2) can be run as plugins on the Torrent Server

If you don't already have a login for the Ion Community site, get that set up and then have a look at the Torrent Browser Plugin Store. The forums on that site are a good help resource for IT-specific tools.

Alex

byou678 · 10-15-2012, 08:54 AM

Thanks very much for your info, arolfe.

Quote:

Originally Posted by arolfe

Mostly you can use whatever tools you'd use for data from another platform. The PGM gives you a FASTQ or SFF file that you can pass to your favorite mapping/assembly/whatever program.

There are some Ion Torrent specific or adapted tools that
1) may provide better results because they've been tuned for the PGM's error model
2) can be run as plugins on the Torrent Server

If you don't already have a login for the Ion Community site, get that set up and then have a look at the Torrent Browser Plugin Store. The forums on that site are a good help resource for IT-specific tools.

Alex

simobioinfo · 11-20-2015, 03:18 AM

Hi,
anyone tried to analyze simulated data with torrent suite installed on a personal server?

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10-11-2012, 02:07 PM	#1
byou678 Member Location: Maryland Join Date: Aug 2011 Posts: 52	Ion Torrent PGM Analysis Pipeline Hi Everyone, If anyone has Ion Torrent PGM data analysis experience here, could you please share your general/standard Analysis Pipeline? Thanks for any response!! In addition, what kind of software do you mostly use? Our department typically uses Partek and Galaxy. Any other recommended software based on your Pipeline?

10-11-2012, 02:54 PM	#2
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	Don't crosspost. Deleted your other thread. Thanks!

10-12-2012, 09:18 AM	#4
arolfe Member Location: 02119 Join Date: Jul 2011 Posts: 29	Mostly you can use whatever tools you'd use for data from another platform. The PGM gives you a FASTQ or SFF file that you can pass to your favorite mapping/assembly/whatever program. There are some Ion Torrent specific or adapted tools that 1) may provide better results because they've been tuned for the PGM's error model 2) can be run as plugins on the Torrent Server If you don't already have a login for the Ion Community site, get that set up and then have a look at the Torrent Browser Plugin Store. The forums on that site are a good help resource for IT-specific tools. Alex

11-20-2015, 03:18 AM	#6
simobioinfo Member Location: italy Join Date: Aug 2014 Posts: 38	Hi, anyone tried to analyze simulated data with torrent suite installed on a personal server?