- 3.2GHz 8-core Intel Xeon W processor
- 32GB 2666MHz ECC memory
- 1TB SSD storage
- Radeon Pro Vega 56 with 8GB HBM2 memory
- 10Gb Ethernet
- If we have the above described computer, do you know how long/how well it will be able to process de novo assembly of 300 million 150-bp Illumina reads?
de novo assembly of what organism's genome? rule of thumb is a 1gb of memory per 1mbase of genome size at about 50x coverage.
Thanks so much for your response. The estimated genome size is between 150-250 Mb. We don't really know. Ireneusz mentioned RAM as being important. How does the number of cores figure out in the "equation"? Thanks again!
Hello Jeanmaire,
The bottleneck of de novo genome assembly is the memory. You won't be able to carry out analysis with insufficient RAM. Thus you should invest in it as much as you can.
Another issue is the time of computation. More cores will speed up your analysis if you are going to use software with threaded parallelization implemented. In contrast to RAM, there is no threshold in terms of cores amount that you have to provide to run the analysis. As Ireneusz and Andrea have mentioned before RAM consumption and time of computation depends on characteristics of analysed genome.
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