C. Titus Brown

theory: for optimal sensitivity/specificity tradeoff we want to choose the smallest k-mer size such that no one k-mer is expected to appear more than once per genome. calculation of said...

> Just catching up on this > > > @bluegenes and I were discussing ways to decrease the false positive rate for prefetch/gather when using very low thresholds. > >...

@dkoslicki you might be interested in this line of thinking too - unicity distances. https://github.com/ctb/2022-sourmash-sens-spec/issues/1

one of my (our!) conclusions from digging into the reasons why sourmash performs well in the above paper is that even low thresholds for combinatorial collections of hashes are really...

Answer to a question in the Element/Matrix group: >I have a question regarding the gather and search commands. I am using the default values for the threshold for gather and...

hi @RhettRautsaw sorry for delay - it is almost certainly due to the krona report not using abundances; see https://github.com/sourmash-bio/sourmash/issues/3577 for context. I will look into it! cc @bluegenes

This is being resolved in https://github.com/sourmash-bio/sourmash/pull/3711, which was a bit of a beast to make sense of. But I think I understand it all now and have both documented and...

sourmash v4.9.4 has been released to a pypi and a conda-forge near you!

Hi Gabri, sorry for ignoring your issue for so long 😭 Short version - we don't have anything formal for plants, BUT if you can find a listing of all...

hi @gabridinosauro sorry, we need to format the taxdb for you/make the lineages CSV - there are some instructions in the plant repo mentioned above, but I'm not sure if...