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Is anyone working on this? I am interested in using cloud computing for a de novo Solexa assembly of mammal transcriptome. Looked at Amazon, but they will only dedicate ~15gb RAM per instance/user.
Any ideas? Matt
Any ideas? Matt
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Would it be possible to start up multiple instances and cluster them so they share the RAM? I could be talking rubbish though, as I'm not well versed in EC2 or computing clusters!
There's a test program in the Amazon Elastic Map Reduce called CloudBurst which is supposed to do short read mapping to a reference genome, although I haven't used it, I've only seen the paper. The Amazon info for it is at http://developer.amazonwebservices.c...xternalID=2272. -
That is pretty cool. I'd love to get together a more complete userguide for launching EC2 instances for beginners (myself included).
I know of another similar cloud project that is getting ready to launch...maybe that time is getting closer!
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I am starting to look into this, I'll let you guys know if I get anywhere.--
Senthil PalanisamiComment
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Hi Matt,
I've talked to Amazon Web Services and it sounds like a viable option for running a distributed-RAM method like ABySS. Pretty affordable too. They recommended a contractor to me who has experience setting up MPI-enabled jobs on EC2 which would be necessary to do ABySS.
I believe they are also going to get some larger-RAM machines available in the near future.
Best,
KristenComment
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Hi,
You can use the "High-Memory Quadruple Extra Large Instance" instance type, which comes with 64GB of RAM and costs $1.8 per hour:
For prices, see http://aws.amazon.com/ec2/pricing/Comment
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Hi,
If there are enough interests on a user guide on how to get starting with Amazon EC2, I can put one together.
QComment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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