Ion Torrent PGM Analysis Pipeline

[byou678]

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]

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

[byou678]

Done. Thanks.

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

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

[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

[byou678]

Thanks very much for your info, 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]

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