Hi all - I'm getting (my first) Ion Torrent data set from a collaborator. It appears I have to use the Torrent Suite application which is only available on the Ion Torrent Cloud or downloaded as a VM. Are there any other options for mapping Ion Torrent data?
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Originally posted by GenoMax View PostIon torrent can produce normal fastq format files as one of the options. You should be able to use any standard mapping program with these files.
Compressed SFF, Fastq files can be downloaded off the server to be used in your favourite applications, or an alignment can be run on the server giving you a bam file
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After talking with some of the Ion Torrent reps, they recommend using TMAP and their own variant caller. Information can be found at the Ion Community (requires signing up). Both their aligner and variant caller can use the flow intensity information and have been optimized for their sequencer, so could possibly give you better alignments and calls than a pipeline optimized for a light-based sequencer (although I haven't put that to the test).
Justin
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