Question: What is the minimum system requement for oxford nanopore read assembly
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gravatar for nagendranp1991
18 days ago by
nagendranp19910 wrote:

what is the minimum system requirement for assembling long reads obtained from pacbio or oxford nanopore ?

forum assembly • 199 views
ADD COMMENTlink modified 18 days ago by Istvan Albert ♦♦ 78k • written 18 days ago by nagendranp19910
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I would say that the answer will depend on more what you are assembling (complexity of size or population)

ADD REPLYlink written 18 days ago by Istvan Albert ♦♦ 78k

For a 2 gb genome assembly?

ADD REPLYlink written 18 days ago by nagendranp19910

How much data do you have?

ADD REPLYlink written 18 days ago by genomax58k

We haven't sequenced yet. the organism have approximately 2 gb genome size.

ADD REPLYlink written 18 days ago by nagendranp19910
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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.

ADD REPLYlink modified 18 days ago • written 18 days ago by genomax58k

thank you A cluster computing facility is not mandatory right?

ADD REPLYlink written 18 days ago by nagendranp19910
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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.

ADD REPLYlink written 18 days ago by Istvan Albert ♦♦ 78k

nagendranp1991 : This paper would be of interest: https://www.nature.com/articles/nbt.4060

Check the compute section for details on what they used.

ADD REPLYlink modified 18 days ago • written 18 days ago by genomax58k
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