C. Titus Brown

added here - https://github.com/sourmash-bio/sourmash/pull/3422 - should add the t2t ones, too, though.

@ccbaumler suggests adding more animal genomes over in https://github.com/sourmash-bio/sourmash/pull/3422#issuecomment-2525421661: >1. rat https://www.ncbi.nlm.nih.gov/datasets/taxonomy/10116/ > >2. xenopus https://www.ncbi.nlm.nih.gov/datasets/taxonomy/8355/ > >3. zebrafish https://www.ncbi.nlm.nih.gov/datasets/taxonomy/7955/ > >4. drosophila https://ncbi.nlm.nih.gov/datasets/taxonomy/7227/ > >5. c. elegans https://www.ncbi.nlm.nih.gov/datasets/taxonomy/6239/ Rather...

hi @yuzie0314 - yes, the `Killed` means sourmash used too much memory. there is a long issue https://github.com/sourmash-bio/sourmash/issues/2299 about this. we are still in a bit of a confused state...

## matrix vs CSV output hi @yuzie0314, yep, the output of `pairwise` is a different format - this is because the numpy matrix format is not a sparse matrix, and...

hi @yuzie0314 I got inspired by your question (and also by some of my own research needs ;)) and built a plugin that I think will help you - see...

That's a great test! You should get identical results (although I will confess I have not tried it myself). I will try it out on my own set of data,...

I'll have to take a look. Have you compared the Jaccard index or containment matrices, rather than the ANI? I'm wondering if there's a difference in the ANI calculations -...

I am a little bit worried that the ANI numbers in sourmash_plugin_branchwater are incorrect - we are seeing differences in `sourmash gather` output per https://github.com/sourmash-bio/sourmash_plugin_branchwater/issues/331#issuecomment-2168882104. Sorry, just put 2+2 together...

hi! I did some quick validation on a subset of `Thermotoga` genomes I had lying around. ## `sourmash compare --ani --containment` ``` % sourmash compare /tmp/thermo.sig.zip -k 31 --ani --containment...

ok, I sat down and did a much more thorough evaluation over in https://github.com/sourmash-bio/sourmash_plugin_branchwater/pull/366, for the `average_containment_ani` column. This comparison generated `sourmash compare --ani --avg-containment` results and compared them to...