I recently started work in a lab where I have a budget of approximately $20,000 to spend on a workstation. This will be used for analysis of RNAseq data (using Trinity and, later, Tuxedo), as well as for the de novo genome assembly. Our model organism has a genome size of approximately 1 Gb.
I am new to genome assembly, but have read through the manuals of Allpaths-LG, SOAP De Novo, and Velvet and gleaned what I could regarding RAM use. Considering the size of our genome, I created a hardware configuration, with the largest consideration being the amount of RAM.
The configuration I've settled upon is as follows:
Is this sufficient? Or is additional hardware recommended / needed for de novo assembly of a genome of this scale?
I am open to any suggestions / criticisms regarding this configuration. If justifiable, the budget can potentially be expanded, if it is necessary for the aims mentioned above.
Thanks!
I am new to genome assembly, but have read through the manuals of Allpaths-LG, SOAP De Novo, and Velvet and gleaned what I could regarding RAM use. Considering the size of our genome, I created a hardware configuration, with the largest consideration being the amount of RAM.
The configuration I've settled upon is as follows:
- 4 Intel Xeon E5-4620 2.20GHz 8 Core CPUs
- 512 GB memory (32 * 16 GB 1333 MHz RDIMMs)
- 4 1.2 TB 10K SAS drives in a RAID 5 array
Is this sufficient? Or is additional hardware recommended / needed for de novo assembly of a genome of this scale?
I am open to any suggestions / criticisms regarding this configuration. If justifiable, the budget can potentially be expanded, if it is necessary for the aims mentioned above.
Thanks!
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