Software to process IonTorrent data

[Marius]

Does anyone of you have experience with different softwares available for processing Ion Torrent data? Or could you recommend a certain software?

I found these four also suggested on the Ion Torrent page:

http://www.iontorrent.com/products-analyze-data/

Important Features I'm looking for:

- handling of RNA "AND" DNA data
- consensus calling, if possible quality-aware
- SNP and Indel (marker) detection
- comparisons of sequences to detect things like inversions etc.
- if possible: is there a software where one can upload or directly align reads to an existing reference (genome or scaffolds?)!!? -> that would be great
- possible statistical analyses
- graphical (output) applications

I cannot tell from the descriptions of the different software, which one is the "best".
What also influences my choice positively is a user-friendly interface and a software.

What do you recommend?

[Bukowski]

Why not request evaluation copies of all of them? And get some prices? Better to try them out and make sure that not only they do what you want, but in the time you want and with the ease you desire. There's no 'best fit' solution for everyone.

[GenoMax]

Unless you are willing to purchase commercial software (which is what the four examples on that page are) why not use galaxy (http://usegalaxy.org).

[aeonsim]

I've used Real Time Genomics with ion torrent data, it is commercial but there is a free verion for individual use. It's very fast, and easy to use, works on ion torrent + 454 and Illumina data. With the ion torrent data I've got it takes a few minutes to map it to the reference genome.

http://www.realtimegenomics.com/Applications/Sequence-Analysis/Ion-Torrent-Sequence-Analysis

[PenelopeFudd]

LifeTech just released their assembler as open source on GitHub. Here's their announcement, copied from http://lifetech-it.hosted.jivesoftwa.../docs/DOC-2431 (free registration required to see the announcement, not to get the software):
----
Torrent Suite 2.0 Source Code
VERSION 1
Created on: Jan 23, 2012 1:37 PM by Matt Dyer - Last Modified: Jan 23, 2012 1:40 PM by Matt Dyer

I am happy to annouce that the source code for Torrent Suite 2.0, TMAP, Torrent Scout, and the new Ion Variant Caller plugin are now available publically at GitHub. Anyone interested in the source code should get it from GitHub, we will not longer post the source on the community.



Torrent Suite 2.0: http://github.com/iontorrent/TS

TMAP: http://github.com/iontorrent/TMAP

Torrent Scout: http://github.com/iontorrent/TorrentScout

Torrent Variant Caller Plugin: http://github.com/iontorrent/Ion-Variant-Hunter

If you are interested in sharing your changes to our source with the community please see Sharing your Torrent Suite modifications with the Community (http://ioncommunity.iontorrent.com/docs/DOC-2201 )