C. Titus Brown

code updated to run with `Rscript` nicely here - https://github.com/ctb/2022-may-cfde-demo/blob/main/sourmash_gather_to_metacoder_plot.R walkthrough of doing gather + plot with an iHMP sample, here - https://github.com/ctb/2022-may-cfde-demo/blob/main/demo-walkthrough.ipynb full install instructions here - https://github.com/ctb/2022-may-cfde-demo/blob/main/INSTALL.md for...

while working on #2178, a few additions - taxonomy ranks are superkingdom, phylum, class, order, family, genus, and species. strain is allowed in files but is handled inconsistently at the...

note GCF / GCA problem, https://github.com/sourmash-bio/sourmash/issues/2049

see [folksonomies](https://en.wikipedia.org/wiki/Folksonomy) in particular, mentioned in https://github.com/sourmash-bio/sourmash/issues/1916 and https://github.com/sourmash-bio/sourmash/issues/268#issuecomment-305990650

continuing that thought - `sig grep` seems like the places to do this, or perhaps something specific to manifests where we can link signature identifiers/names to generic metadata.

I think expanding standalone manifests to support this kind of thing is the way to go - explicit shoutout to https://github.com/sourmash-bio/sourmash/issues/1916.

agreed with all things :)

We also have a big conceptual dichotomy, where the code *computing* signatures behaves as if each `SourmashSignature` may contain multiple `MinHash` objects, but the code *operating* on signatures behaves as...

I like how you avoided the word "just" in that comment in favor of "quite doable."

as I dug in to `SourmashSignature` a bit more in #1179, I noticed that `md5sum` is calculated on the `sig.minhash` not on the `SourmashSignature` itself. So this is another place...