Hi
We have a hiseq 2000 and manage our own GATK pipeline, grid, storage. We are in the process of purchasing a NextSeq 500 and are worndering if basespace would be a feasable longterm data analysis/housing solution?
If you are an illumina customer, do you use base space? if not can you explain the reason?
ADDENDUM: We do whole exome, tumor/normal (small panels to whole exome), transcriptome, and other 1000-5000 genes custom panels.
Thanks
Manfred
Hello,
Well the answer to your first question depends on what analysis do you actually perform. If those are some in-house pipelines that have no commonly used alternative, then the best solution for large-scale projects is to get familiar with cloud solutions, such as AWS. Note that Basespace "locks" you within its data management system, so you can't easily incorporate custom data processing steps.
As for the second question, in my lab we are currently working in a rather small field that has few publicly available software tools, so we mostly run our in-house pipelines on our server infrastructure (yet we had an idea to submit our apps to Basespace). Occasionally we have to work with big chunks of data sent by our collaborators, so we have developed a pipeline to manage AWS instances for such tasks.
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mikhail.shugay
Thanks Mikhail
I added the apps we run to my question above. Thanks for your feedback. Ours seem to be pretty common workflows that would likely use many of the tools available as basespace apps, however we are still cautious about being "locked in" to their data management/storage/LIMS etc.
+1 for AWS. I've been using it extensively for the past 6 months or so and it has sped up my work tremendously. Here are some tips for using AWS:
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Damian Kao
Also +1 for AWS.
All instances has also local SSD drives (one of them is mounted to /mnt on Ubuntu instances; for example r3.8xlarge has 2x320 GB SSD on board); by using them you can reduce you bills (especially on spot instances) and increase throughput because local drives are installed inside the actual compute node, and are much faster then EBS.
We do it in this way:
/mnt) using AWS CLI.Sometimes we automate all this steps by scripts executed using cloud-init, without accessing instance through SSH.
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bolotin.dmitriy •
I played around with the basespace applications a bit and was pretty unimpressed. From my experience it's not up to the task, though I'm not doing the same applications as you.
For one example, the 16S analysis. It is pretty basic and inaccurate but I thought might give a preliminary idea of our samples. However, it would only work with some limited number of samples at a time (I think 50). If you tried to specify more it just kind of silently failed and only did 50 out of how ever many you specified.
Also Illumina has not responded to support requests.
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Cliff Beall
That's helpful to know Cliff. Did you end up using the results from basespace or were more conformable redoing it with your own pipelines anyway ?
The reason I ask is, I am trying to figure out if
If its the second, then I foresee many new apps being added in near future, but if its the first, then that's a bigger problem
I wish they allowed threading apps together for building workflows/pipelines
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prateek.kr •
I could see the usefulness of that - but unlike seven bridges, they can't ensure that the output of one app will behave nicely going into the next app. Apps are built by 3rd party vendors here
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prateek.kr •
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