C. Titus Brown
C. Titus Brown
hi @Adamtaranto, we downloaded them and deleted them immediately (or, well, never saved them ;)) using the directsketch plugin: https://github.com/sourmash-bio/sourmash_plugin_directsketch. That would be my recommendation! The plugin supports saving the...
hi @jodyphelan, some hot takes per @bluegenes (who wrote this part of tax): >that's complicated. Basically yes, if we believe we have the "right" ANI/AAI cutoff for genus-level matching You...
@jodyphelan this looks great! I will say that an 11.1% overlap in k=21 space between microbial genomes is actually surprisingly stringent (despite looking "low") and would match ~family or genus...
This is relevant - https://github.com/sourmash-bio/sourmash/issues/3694
hi @jodyphelan I did some experimenting. First, build a manifest from GTDB rs226: ``` sourmash sig collect gtdb-rs226-reps.k21.sig.zip -F csv -o out.csv ``` next, manually edit `out.csv` to remove any...
Hi @jodyphelan finally found this in my inbox ;). The only danger of using a small database is that contaminants and unexpected hits won't be found. Also, in re memory...
I'll close this for now - feel free to reopen or post a new issue!
the actual error text is above your copy/paste ;). it would be good to isolate the cause of this. I haven't tested it myself, yet, but it absolutely should work....
Yeah, the problem seems to be fastgather, point 1. Sigh.
related issues: * https://github.com/sourmash-bio/sourmash/issues/3577 * https://github.com/sourmash-bio/sourmash/issues/3598