ion torrent barcode sequences

[[email protected]]

I am trying to discover the sequences of the barcodes used in the ion Torrent barcoding kit. The Torrent Server doesn't sort files by barcodes unless you are doing genome sequencing for some weird reason, so for sequencing environmental amplicons I will have to do this with a script. However, the barcodes on the Torrent Server software are 11 bp long, the barcode kit manual says the barcodes are 10 bp long and nobody at Life Tech seems to be able to provide any information on this, in keeping with their apparent policy on keeping everything about this system as secret as possible. If anyone has more knowledge than me on this, I'd be grateful for them to share it.

PS: Anyone want to buy a slightly used Ion Torrent?

[IonTorrent]

Hi Simon,

I believe your questions have already been answered and I've also sent you a PM. None of what you've asked for is secret information. My sincere apologies if you've encountered any delays in getting the information you needed.

[[email protected]]

Very competitive pricing...

[singaporeseq]

Why are you selling?

[kenietz]

Hi,
how can one manually separate the reads by barcodes coming from the PGM? We got FASTQ and SFF but the reads are not separated by barcodes. Is there a tool or script or something?

Thank you

[[email protected]]

There is a bug in the Torrent Server software as of the current 1.5 version that means that it won't sort barcodes for you unless you specify a reference sequence to compare against, even if you don't have one for your amplicons / fragments. If you have done a run with barcoded adapters/fusion primers then you can re-analyse it on the Torrent Server making sure you tick the 'reference' sequence for the E.coli control sequence. It will then give you separate FASTQ files for each barcode.

Another option is just to use a script to do it yourself. This lab has produced a good bunch of scripts for this and other sequencing processing tasks:

http://hannonlab.cshl.edu/fastx_toolkit/

[kenietz]

Hi Simon,
thank you very much for the fast and informative answer. I will check the scripts for sure and will tell the lab guys to do as you suggested for next runs.

Cheers

[Retro]

designing Ion Torrent barcode sequences

Are there any rules how to design new barcodes for Ion Torrent? We have used successfully our 454 amplicon primers, but now we have to add more primers. I am not sure, but the barcode sequence is optimized for the order of nucleotide flow? Is this known for Ion Torrent and are there any public lists of IT barcodes (for 454 there are many)?

[Fisher.R]

ion seq

Hi Simon,

I believe your questions have already been answered and I've also sent you a PM. None of what you've asked for is secret information. My sincere apologies if you've encountered any delays in getting the information you needed.

Hi there Ion man.
I planning an IT experiment with HIV seq but I'm also struggling to find the barcode sequences. Could please send me a link or maybe the sequences?

Best regards.
RF.

[IonTorrent]

Hi there Ion man.
I planning an IT experiment with HIV seq but I'm also struggling to find the barcode sequences. Could please send me a link or maybe the sequences?

Best regards.
RF.

Hi RF,

you can find the full set of 96 barcodes (adaptors with barcodes 1 - 16 and 17 - 32 are available as commercial kits if that option is of interest) at this location on the Ion Community:

http://lifetech-it.hosted.jivesoftware.com/docs/DOC-2346

[IonTorrent]

I should also mention that as announced today, the full set of 96 barcoded adapters is now available as a kit (Ion Xpress™ Barcode Adapters 1-96 Kit):

http://products.invitrogen.com/ivgn/product/4474517

[ChrE]

Greetings all,

Thanks for the info!

If e.g. the barcode 1 oligos are aquired then, how should these be prepared and at what concentrations?
Should the long and short sequences just be diluted to an appropriate stock concentration and then simply mixed together or should they be pairwise annealed somehow prior to ligation (or perhaps just ordered as a duplex)?

Throughout all available manuals and guides only adapter volumes seem to be mentioned, but I haven't been able to find a single place where the actual concentration of the adapter solutions are mentioned in any of these manuals. Does anybody know what concentrations should be used? (I.e. what are the stock concentrations in the Ion Xpress barcode adapter kits)

Also, I do not understand why the overlap between the barcode adapters are not similar to the overlap between the non-barcoded adapters, i.e. in the non-barcoded adapters there is a T*T* overhang from the complementary sequence while there is a 13-base non-overlapped sequence in all the barcoded adapters. Why might this be so?

Best regards

[jyheo]

Hi RF,

you can find the full set of 96 barcodes (adaptors with barcodes 1 - 16 and 17 - 32 are available as commercial kits if that option is of interest) at this location on the Ion Community:
http://lifetech-it.hosted.jivesoftwa.../docs/DOC-2346

Dear all,

I am analysing public whole genome data produced by Ion Torrent and currently looking for information of adapter sequences.
I contacted Thermofisher refering to this thread to request the information of barcode sequence, but like Simon, they only replied that it was confidential.
They claim that the adapter seq is trimmed at the data before providing to customers, but in the data, I found some insertions presumed to be adapter sequences repeatedly.
It seems that the information was previously open, so it would be nice if I could still access the informatino.
Can anyone help about it?

Thanks,
Jun-Yeong

[snetmcom]

all adapter and barcode sequences are in your torrent suite admin page. nothing is hidden.