David Koslicki
David Koslicki
@s-yata Any chance this ancient issue will be addressed? I'm running into the same problem
@bluegenes I wouldn't expect the de-biasing to cause large changes. It really only comes into play when the underlying sequence set is very small. And agreed this seems suitable for...
To chime in on this issue, I spent a while being misled by this too: I thought I was using the `--merge` flag incorrectly. Would be nice to know/be warned...
@moritzbuck We have yet to track down what exactly is causing that little tail for FracMinHash-based ANI (in your plot around 0.85 ANI). In one set of experiments, [Figure 2a...
Yup, that's what I would suspect too. I can't seem to find it now, but I recall that plot you had of containment vs k-mer size and ANI vs k-mer...
Yup, that's the one!
From a philosophical perspective, I think this is good evidence that ANI is more interpretable than containment/similarity. How large of a containment value is considered "big" depends quite a bit...
It looks like I'm using 2.1.1 (which is what ``pip install khmer`` gives). Good to know about ``n_unique_kmers`` versus ``n_occupied``; the source of my confusion was the fact that (when...
Thanks @ctb; I am already forming the `Nodegraph`'s, so thought `n_unique_kmers` would be a handy way to circumvent repeat calculations.
Old issue, but I received the same error, but found the following solves the issue: ```install_from_swirl("Mathematical_Biostatistics_Boot_Camp")```