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Old 07-16-2014, 12:24 PM   #1
jae_63
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Location: Bethesda, MD

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Default remotely controlling/monitoring Illumina instruments?

Hi,

I'm working with a client who needs to remotely access information about a sequencing run, on various instruments. For example, one can readily do this for an Ion Torrent, by reading the documentation and subsequently testing with their virtual machine, as described here:
https://github.com/iontorrent/TS

While it's unlikely that such extensive resources are available for Illumina instruments, I would appreciate some information regarding how one might monitor progress, assuming that I could install a little bit of additional software (e.g., to rsync some files to the monitoring host) on the instrument hardware itself.

In particular, it would be nice to be able to fetch the instrument's current operating parameters, as well as information regarding progress through the current run, etc. My guess is that this would be different for, say, a NextSeq as compared with a HiSeq or MiSeq.

Assuming that there are no friendly APIs such as the Ion Torrent provides, then a good starting point would be to understand how the relevant information could be retrieved if I had an open Unix shell running on the instrument hardware itself.

My current focus is Illumina, but any similar information regarding other commonly used instruments such as PacBio would also be helpful.

Thanks in advance ...

Jonathan
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Old 07-16-2014, 02:04 PM   #2
GenoMax
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Look for "Can I remotely monitor my run?" here: http://support.illumina.com/sequencing/faqs.ilmn

You could rsync "InterOp" directory from a flowcell folder (and *.xml files) to a file location. Your client can then use Sequence Analysis Viewer to view the data: http://support.illumina.com/sequenci...iewer_sav.ilmn I believe someone else had written a different application (search SeqAnswers) to parse these files in case you do not want to use windows based software.

If these instruments are connected to BaseSpace (which I assume they are not otherwise you would not have asked this question) then you can use that to remotely monitor runs: http://www.illumina.com/informatics/...anagement.ilmn
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Old 07-16-2014, 02:38 PM   #3
jae_63
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Thanks, GenoMax, this looks like incredibly useful information ... just what I needed to get started.



Jonathan Epstein
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Old 07-20-2014, 06:36 PM   #4
ScottC
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When you say that you want to "remotely monitor" runs, what exactly are you wanting to do?
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Old 07-21-2014, 02:40 PM   #5
jae_63
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Quote:
Originally Posted by ScottC View Post
When you say that you want to "remotely monitor" runs, what exactly are you wanting to do?

Thanks for your post Scott. I haven't yet defined the scope beyond what I've written above. I'm wrestling with the Ion Torrent Server for now. Once I've done that, and pursued the Illumina equipment as suggested by GenoMax, then I'll have a clearer sense as to what generic information I can retrieve from different instruments.

But overall the goal is to monitor a sequencing run, and integrate the available sequencer-derived data with an external database which tracks the provenance of the samples which are being run. Being able to integrate this data with other Quality Control assays such as BioAnalyzer runs is also one of my goals.
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