Question: Trinity run time
gravatar for Bioinformatics_finn
7 months ago by
Bioinformatics_finn0 wrote:

Hey y'all,

I'm currently trying to make sense of the run time that it takes trinity to assemble a transcriptome. I know the general estimation for assembling the transcriptome is that it will take .5 to 1 hour per million reads.

I understand that if I had 40 million reads it should theoretically take 20-40 hours for Trinity to assemble the transcriptome. Does this mean that if Trinity was ran on 10 CPU cores that it should theoretically take 2-4 hours for the transcriptome to be assembled (barring any technically limiting steps) since the processing would be spread across the 10 cores?

Thank you all in advance.

rna-seq trinity • 287 views
ADD COMMENTlink written 7 months ago by Bioinformatics_finn0

Do you have access to a cluster, or machine with more compute threads? Test it, provide feedback.

ADD REPLYlink written 7 months ago by

I am not sure if one would be able to estimate run time for a process like Trinity unless you actually run a real test since much of this may depend on the hardware you have access to/complexity of your dataset. You also need 1G of RAM per million PE reads so that may also become a limiting factor.

Practically, start with as much resources as you can use instead of trying to estimate the run times.

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax42k
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