-
Notifications
You must be signed in to change notification settings - Fork 1
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
What should we benchmark? #232
Comments
It would also be interesting to compare the accuracy of |
It sounds like you might be trying to benchmark both computational performance and classification performance. Those are pretty different things. I don't think that charcoal has any individually expensive steps or computationally complex scripts that are part of it; it's just the workflow overall that involves an awful lot of steps, much like genome-grist. That may change your benchmarking strategy. |
I agree! They are completely different benchmarks. Mostly wanted to jot down the notion before it left me forever. Would you suggest forking and adding |
Following the same process as sourmash-bio/sourmash#2410, we will benchmark the charcoal workflow with the demo directory and/or the six signatures included in sourmash-bio/sourmash#2410. Suggesting to:
It may be interesting to also compare the results of
sourmash search --containment
to `charcoal.contigs_list_contaminents.py in this repo.The text was updated successfully, but these errors were encountered: