C. Titus Brown

can / should this issue be closed? @bluegenes

I'm pretty sure it's related to https://github.com/sourmash-bio/sourmash/issues/1899. Will think on't.

See #3637 - try using `--from-file` instead of just specifying the path list i.e. ``` sourmash sig check --from-file pathlist.txt ``` should do the right thing, while ``` sourmash sig...

This could perhaps be done by upgrading `combine_csv` to support redundant idents in multiple files, processed in file order. Then custom genome name(s) could be given that way.

I mean I've loved pixi, the little bit I've used it; but do we really want to switch dev instructions over to it?

(I guess I'm not immediately seeing a big reason. But I am happy to be convinced :)

## Review checklist for @ctb ### Conflict of interest - [x] As the reviewer I confirm that I have read the [JOSE conflict of interest policy](https://github.com/openjournals/joss/blob/jose/COI.md) and that there are...

> [@ctb](https://github.com/ctb) thank you for completing your review checklist. Please let us know if you have any other feedback beyond the issues already raised in [@NickleDave](https://github.com/NickleDave) 's review. I'm watching...

They're linked here, https://github.com/sourmash-bio/sourmash/issues/3504, for k=51 - from late Jan 2025. They are actually available at k=21, 31, and 51 - https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/genbank-euks-2025.01/fungi.k21.sig.zip https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/genbank-euks-2025.01/fungi.k31.sig.zip https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/genbank-euks-2025.01/fungi.k51.sig.zip I'm not sure what to say...

Excellent, always what we like to hear 😆 I think nr/nt is _all_ sequences, not just features annotated on assembled genomes. That includes targeted gene sequencing from Sanger etc, too.