Closed mbhall88 closed 1 year ago
Okay, so this is what I have for the nanopore data. Anything we want changed?
Nice visualisation
On Wed, 12 Oct 2022 at 16:30, Michael Hall @.***> wrote:
Okay, so this is what I have for the nanopore data. Anything we want changed? Runtime
[image: image] https://user-images.githubusercontent.com/20403931/195257678-cde00e5c-8d00-4b2b-b807-cd266b75e77a.png Max. RAM usage
[image: image] https://user-images.githubusercontent.com/20403931/195257695-4863394e-9a86-4c5c-9c9c-d1c1365a2854.png
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Looks great. Nothing to change, though I'm wondering what the p values are testing
Just testing whether the means of the distributions are equal. Pretty clear they are not from the plot but I guess it helps if you want to say "significantly different" . I guess you used an unpaired t-test, but actually they are paired data (same sample using different approaches) If anything that should make the pvalues even more significant.
On Wed, 12 Oct 2022 at 17:40, Zamin Iqbal @.***> wrote:
Looks great. Nothing to change, though I'm wondering what the p values are testing
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I used a wilcoxon signed-rank test. Basically the nonparametric version of a paired t-test (because I'm lazy and couldn't be bothered testing for normality 😅 )
Pretty clear they are not from the plot but I guess it helps if you want to say "significantly different"
It wasn't actually clear to me that the runtimes would be significantly different for drprg and mykrobe
Here are the Illumina figures. These aren't final as this is only a subset of 400 samples, but I can't imagine it will change dramatically.
The latest figures after adding in the racon denovo from https://github.com/rmcolq/pandora/pull/299 can be seen in https://github.com/rmcolq/pandora/issues/303#issuecomment-1305098855
Create benchmark figures for time and memory usage.
How do we want to do time? CPU time, wall time? I guess this gets complicated by threads, although I am using 2 for each tool at the moment.