Workstation requirement for running Trinity assembly

[Rukmankesh Mehra]

Hye,

I'm new to transcriptome assembly. We are planning to buy a HP workstation where we can run transcriptome assembly using Trinity. Please suggest the system requirement for the optimum software performance.

How many number of CPUs (cores) are required when using 256GB RAM? With 256GB RAM, how much time it would take to complete the assembly of 30 million reads?

I read that 1GB memory per 1M reads is required, and it takes 1/2 to 1 hour to assemble 1M reads. Does this mean that 30 million reads will be assembled in approximately 30 hours (with 30GB of RAM)? 

  

[Brian Haas]

Before buying hardware to run Trinity, you might just try to use our existing Galaxy service:

 https://galaxy.ncgas-trinity.indiana.edu/user/login

It's free.

If you decide to buy hardware, a 256GB RAM server with 4 or 6 CPUs would be fine for a lot of work, but a 512GB server would be better if you could afford the extra RAM.

We have only very general guidelines for expected runtimes and hardware needs - and there's a lot of variability there depending on the complexity of your sample.

best,

~b

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[Rukmankesh Mehra]

Thank you Dr Brian Haas for your suggestion. I will definitely go through the Galaxy server. How much approximate time is required in Galaxy server to assembe 30M reads? 

 I'm really concerned about the time consumption for the transcriptome assembly. As you suggested that the time may vary depending up on the complexity of the data, but can you suggest me the approximate time required so that I can configure my hardware accordingly. 

 

Right now we can afford only 256GB RAM server. You suggested to use 4 to 6 CPUs. Please also suggest the required number of cores per CPU and the clock speed of each CPU?

 

  

[Mark Chapman]

I have no experience configuring a server but 30M isn't a lot so I wouldn't be concerned about it needing all your memory and all your cores.

BW, Mark

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[Brian Haas]

You're over-thinking this purchase with respect to Trinity.  There isn't anything 'special' required for it beyond being a high-mem multicore server.  I'd suggest just making sure you buy decent general purpose hardware, and go with some Intel processors - just get the best you can afford within reason, and go with a trusted vendor (eg. Dell).

Also, unless you have specific reasons for needing to run the Trinity assembly on your own hardware, there are free options for running it elsewhere.

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[Rukmankesh Mehra]

Thank you for the response and useful suggestions. I have already applied for the account in the Galaxy server, and the account will be activated within one week. After activation, I'll go through the Galaxy server for assembly.  

Best

 Rukmankesh