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Old 03-15-2019, 12:52 AM   #1
sanderson83
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Location: UK

Join Date: Mar 2019
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Default Denovo assembly system resources

Hi,

Hope someone can help me out with an IT/Systems question.

I currently process fastq files using Trinity for assembly and this roughly takes 4 hours per sample. I have noticed that throughout this time CPU use almost 100% whilst RAM usage maxes out at around 70%.

I am using a standalone workstation with 2 six core processors and 96 Gb RAM. I have access to 5 of these currently and they are all used independently. This is the system I inherited from my predecessor so I am open to change should it increase throughput.

My question is....

Would creation of a small beowulf style cluster using four of the workstations, allow increased system resources and perhaps speed up my assembly and processing time.

I am no overly familiar with the IT infrastructure side of this so any advice would be appreciated.

Thanks in advance.
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Old 03-15-2019, 04:28 AM   #2
Bukowski
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Location: Aberdeen, Scotland

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Default

I wouldn't have thought so. You require all the reads to assemble the genome, so splitting this across a cluster, without a shared/distributed memory model, doesn't fit the assembly paradigm which is why most people use a big box with lots of RAM.

See:
https://ieeexplore.ieee.org/document/6165266
https://www.hpc.informatik.uni-mainz...nome-assembly/
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