For my MSc internship I am using qiime2 to analyse the gut microbiome of chickens.
I was reading up on the runtime of the q2 fragment insertion command and was wondering whether my current analysis would be too extensive to run on my own computer (Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz 1.80 GHz, 8GB RAM)
I am analysing 12 samples which have been sequenced with novaseq6000
I have attached the table computed from the feature-table summary to this message
table.qzv (458.3 KB)
what runtime could I expect while running fragment-insertion? If this runtime is very long: is it possible to "crop" my data, and furthermore, is this scientifically allowed? what would you advise me to do?
I hope you can advise me in my first microbiome research!
Thank you in advance!
The runtime will vary significantly based on several factors - the data you're placing on the tree, the tree itself, and the host computation environment. The host computation environment specs you have shared here are probably the absolute minimum you can safely use - if you have access to an institutional HPC I would recommend utilizing that.
This method can be particularly slow, especially if you only are running with one thread/core/job, in which case you can expect 10s to 100s of hours, in my experience, but others might have a different perspective.
Yes, we have an extensive filtering tutorial:
It depends on your study design.
Consult your local statistician to help evaluate your current goals/hypothesis, with respect to your available data. Ideally you would do this prior to sampling/sequencing.
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