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Old 11-04-2012, 07:06 PM   #1
golharam
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Default Ion Torrent Mappers

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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Old 11-04-2012, 07:08 PM   #2
golharam
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I see TMAP on github...https://github.com/iontorrent/TMAP

I think I'll try that.
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Old 11-05-2012, 03:48 AM   #3
GenoMax
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Ion 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.
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Old 11-05-2012, 08:54 AM   #4
maubp
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You can also try tools for mapping Roche 454 SFF files, in many ways the Ion Torrent data behaves similarly.
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Old 11-05-2012, 12:26 PM   #5
jimmybee
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Quote:
Originally Posted by GenoMax View Post
Ion 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.
As GenoMax said.

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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Old 11-05-2012, 02:26 PM   #6
BAMseek
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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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Old 11-06-2012, 06:35 AM   #7
adaptivegenome
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We tried TMAP versus BWA-SW and found that TMAP works best for us. I don't know if other mappers perform better.
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Old 11-07-2012, 06:06 PM   #8
timydaley
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Bowtie2 should be able to map the data too. In their paper they compare Bowtie2 to BWA-SW for a Human IonTorrent data set, and I believe they performed similarly.
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