Ion Torrent Data Analysis

RonanC · 07-05-2012, 10:20 AM

Hi everyone,

I wanted to start a thread to get an idea what other ion torrent users are using/doing for their downstream data analysis. There are a number of preferred software vendors suggested by ion torrent including DNASTAR, Avadis NGS, Partek and NextGENe. Has anyone used these and do you have any recommendations? I am in the process of trying a few of them out and wanted to hear what other people thought.

I suppose whatever software you select depends on the type of work you are doing. I work in a microbiology lab so we will be doing some genome sequencing (so assemblies of genomes and alignments against a reference), RNA-seq (looking at transcript geography and expression levels) and possibly some ChIP-seq. I would be particularly interested to hear from other microbiologists who are doing similar work on the ion torrent but any feedback is welcome.

Cheers,

Ronan.

byou678 · 08-07-2012, 08:40 AM

https://learn.appliedbiosystems.com/...ctorsequencing
You can find Web-Based Training in the link above. Best wishes.

leogg23 · 08-07-2012, 04:55 PM

I am trying to detect rare variants in pooled mutated samples. I have barcoded my pools and I have 3 genes I am analyzing in each of 28 pools. Since I am doing this as a test with diluted samples bearing a known mutation I can confirm if the technique is working. I can clearly see the expected mutations (around 2% change), but also see a bunch of sequencing errors, mainly at the end of the reads, which at the end show frequencies close to the real mutation. I been struggling for the last couple of days with SAMtools, CRISP and even the ion torrent variant call plugin without success (this lat one only calls alleles with a minimum of 5% frequency and rare mutations are lower than that. I know there are other Biologist-friendly tools out there, but they are usually expensive, so I am also on the lookout for something free and efficient.

I would mainly like to find a way to tell those sequencing errors from the real variants...any advise?

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07-05-2012, 10:20 AM	#1
RonanC Junior Member Location: USA Join Date: Jul 2012 Posts: 8	Ion Torrent Data Analysis Hi everyone, I wanted to start a thread to get an idea what other ion torrent users are using/doing for their downstream data analysis. There are a number of preferred software vendors suggested by ion torrent including DNASTAR, Avadis NGS, Partek and NextGENe. Has anyone used these and do you have any recommendations? I am in the process of trying a few of them out and wanted to hear what other people thought. I suppose whatever software you select depends on the type of work you are doing. I work in a microbiology lab so we will be doing some genome sequencing (so assemblies of genomes and alignments against a reference), RNA-seq (looking at transcript geography and expression levels) and possibly some ChIP-seq. I would be particularly interested to hear from other microbiologists who are doing similar work on the ion torrent but any feedback is welcome. Cheers, Ronan.

08-07-2012, 04:55 PM	#3
leogg23 Junior Member Location: Edmonton, Canada Join Date: Aug 2012 Posts: 4	also looking for the best way to filter and analyze data I am trying to detect rare variants in pooled mutated samples. I have barcoded my pools and I have 3 genes I am analyzing in each of 28 pools. Since I am doing this as a test with diluted samples bearing a known mutation I can confirm if the technique is working. I can clearly see the expected mutations (around 2% change), but also see a bunch of sequencing errors, mainly at the end of the reads, which at the end show frequencies close to the real mutation. I been struggling for the last couple of days with SAMtools, CRISP and even the ion torrent variant call plugin without success (this lat one only calls alleles with a minimum of 5% frequency and rare mutations are lower than that. I know there are other Biologist-friendly tools out there, but they are usually expensive, so I am also on the lookout for something free and efficient. I would mainly like to find a way to tell those sequencing errors from the real variants...any advise?

08-07-2012, 08:40 AM	#2
byou678 Member Location: Maryland Join Date: Aug 2011 Posts: 52	https://learn.appliedbiosystems.com/...ctorsequencing You can find Web-Based Training in the link above. Best wishes.