Ion Torrent Suite

[icymiktreize]

Hello,
I am totally new in the NGS field, so I have several silly questions. I hope I can have a clearer pictures with your help.
I have my Ion Torrent data and now trying to analyse them. I was suggested to use Ion Torrent Suite, but it is now on the cloud. I have already had an account on their cloud, but the problem is I don't know where to stat first. I could not find any link to download Ion Torrent Suite on their website.
Is there anyone patient enough to tell me what i should do. I really appreciate about that.

[sophiespo]

You can try Ion Reporter, it's free to a point.

https://ionreporter.lifetechnologies.com/ir/

I don't think you can just download Torrent Suite, it usually ships with their servers (I could be wrong).

Your can also use different software, if you are new to this I would read the GATK best practices workflow, it will give you a good understanding of what you have and what you probably want.

http://www.broadinstitute.org/gatk/guide/best-practices

(Click on DNAseq)

[GenoMax]

Torrent suite is available as a free download at this link: https://github.com/iontorrent/TS. If you are not computer savvy, then you may want to stick with the cloud version.

I would think that the ion community site should have tutorials available to use Torrent suite in the cloud. You will have to create a free account to access that forum: http://ioncommunity.lifetechnologies.com/welcome

[icymiktreize]

You can try Ion Reporter, it's free to a point.

https://ionreporter.lifetechnologies.com/ir/

I don't think you can just download Torrent Suite, it usually ships with their servers (I could be wrong).

Your can also use different software, if you are new to this I would read the GATK best practices workflow, it will give you a good understanding of what you have and what you probably want.

http://www.broadinstitute.org/gatk/guide/best-practices

(Click on DNAseq)

Thank you for your answer. But I could not access to the first link.
Do you think GATK is suitable data as many people think it doesn't work well with Ion Torrent data?

[icymiktreize]

Torrent suite is available as a free download at this link: https://github.com/iontorrent/TS. If you are not computer savvy, then you may want to stick with the cloud version.

I would think that the ion community site should have tutorials available to use Torrent suite in the cloud. You will have to create a free account to access that forum: http://ioncommunity.lifetechnologies.com/welcome

I cannot find any tutorial for using Torrent Suite in the cloud. I am not computer savvy but I am willing to learn as long as I know how to start with. From what I understand, I have to download all the source code from GitHub. Then, using Ubuntu with complex command lines to build the Torrent Suite on my computer. Is it right?

[GenoMax]

From what I understand, I have to download all the source code from GitHub. Then, using Ubuntu with complex command lines to build the Torrent Suite on my computer. Is it right?

Roughly yes. Get help from a local friend (who preferably knows about unix) to make this easier.

Have you tried to contact Ion Tech support to see if they can point you to a user guide for the TS cloud version?

[NextGenSeq]

The easiest way to proceed is to generate FastQ files. Then you can use any data analysis pipeline.

[IonTom]

What is you application ?
Are you doing amplicon sequencing of humans ?
More cohorts or single samples ?

You could use another alignement algorithm lile BWA-MEM, Nextgenmap,GEM or Mosaik.
All of which work for Ion Torrent data.

For Variant Calling Free Bayes is what the IonSuite uses.
I am currently using Platypus and the deepSNV bioconductor package.
The VariantTools package is then used for further QC checks of called SNPs


I would not worry too much about GATK, as it it incredibly slow and things
and not all tools work for Ion Torrent data.

Compiling the Torrent Suite can be problematic as it seems to need Ubuntu 10.4.

[icymiktreize]

Thank you very much for your help. I am sorry for not responding for a long time. I am not giving up using Ion Torrent Suite. Now I am using other tools as you guys suggest here. It may take time for me to analyse my data. It is amplicon sequencing.

[cuiya2013]

Do you have any tools to convert dat to fastq?

[snetmcom]

Do you have any tools to convert dat to fastq?

Only the torrent suite can analyze a .dat file. The dat file is completely raw data. there is no sequence information until it is processed by the Torrent Server.