The Ion Torrent next generation sequencer can be purchased with an analyzer (The Ion S5). I was wondering if there is third party software, which you can use to analyze the data obtained from the Ion Torrent in another computer.
You can use any free or commercial software that takes BAM/FASTQ raw files as input. A popular solution is the GATK toolkit for LINUX/UNIX, while the Galaxy framework (usegalaxy.org) offers access to OS-independent web-based tools (you can also add your own). However, there are platform-specific details that you have to keep in mind, like Ion Torrent's inherent homopolymer problem. I'd suggest starting with the inbuilt Torrent Suite Variant Caller, since it has been designed to offset those problems, and if you think there's more information in your results than you are getting this way you can add third party tools into the analysis.
We have been using gatk and samtools for our ion torrent data and never had issues with it. I think it's totally fine to use them as long as you have a pipeline that's best for your biological system.
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