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6.5 years ago
nagendranp1991
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What is the minimum system requirement for assembling long reads obtained from pacbio or oxford nanopore?
What is the minimum system requirement for assembling long reads obtained from pacbio or oxford nanopore?
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I would say that the answer will depend on more what you are assembling (complexity of size or population)
For a 2 gb genome assembly?
How much data do you have?
We haven't sequenced yet. the organism have approximately 2 gb genome size.
In general, human genome can easily require a terabyte of RAM (or more) for de novo assembly so that should give you some idea. Having plenty of RAM would be a key. If your genome has repeats, ploidy (other then standard haploid/diploid) that would add to the complexity of this task.
Doing a
de novo
assembly with only long reads (which are going to have a high error rate 10-15%) is probably not recommended for a genome of this size. You would want to throw in some short read coverage as well.thank you A cluster computing facility is not mandatory right?
Cluster computing facility is actually no help here. A typical cluster architecture is designed to provide lots of CPU nodes but cannot give you more memory than what a given node already has.
nagendranp1991 : This paper would be of interest: https://www.nature.com/articles/nbt.4060
Check the compute section for details on what they used.