C. Titus Brown

>Error: The 'mode' input is required as of CodSpeed Action v4. Please explicitly set 'mode' to 'instrumentation' or 'walltime'. Before, this variable was automatically set to instrumentation on every runner...

note that this functionality is not trivial, and enabling this kind of general query is in fact one of the works-in-progress that https://github.com/ctb/2017-sourmash-revindex and #604 is devoted to :)

(not trivial doesn't mean it's hard; we have several implementations of such a thing, including e.g. https://github.com/ctb/2017-sourmash-revindex/blob/master/hashes-to-numpy-2.py)

It would now (as of #946) be very easy to add a filtering option to `LCA_Database` to support this functionality.

similarly for #1808 and `SqliteIndex`, this is quite easy there.

is now generically available as a plugin: https://github.com/ctb/sourmash_plugin_commonhash also ref https://github.com/sourmash-bio/sourmash/issues/2383

see also https://github.com/sourmash-bio/sourmash_plugin_betterplot/ which has various nice utilities for this, including `--cut-point`.

@luizirber is exploring this in his thesis. the [charcoal project](https://github.com/dib-lab/charcoal) is exploring decontamination in bacterial/archaeal genome bins, while the [2020-long-read-assembly-decontam](https://github.com/ctb/2020-long-read-assembly-decontam project is exploring decontamination in long-read assemblies. I don't think...

hmm, that could indeed be a problem! We do have a `--distance` output for `sourmash compare` so it would be an easy fix.

> I should point out, that in terms of maintaining meaningful relationships, this doesn't seem to be that impactful. In other words, instances that are similar to one another will...