C. Titus Brown

new GTDB databases for rs220: draft

2

**Note: not yet final** release rs220 from GTDB: https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/ sourmash databases constructed by @ccbaumler 🎉 using [directsketch](https://github.com/sourmash-bio/sourmash_plugin_directsketch) - * [gtdb-rs220-k21.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs220/gtdb-rs220-k21.zip) - 17 GB * [gtdb-rs220-k31.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs220/gtdb-rs220-k31.zip) - 17 GB * [gtdb-rs220-k51.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs220/gtdb-rs220-k51.zip)...

pyodide + sourmash thoughts

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per https://github.com/sourmash-bio/sourmash/issues/2553#issuecomment-1506094767, we can run sourmash in the browser like so: > - Go to https://pyodide.org/en/latest/console.html > - Use `micropip` to install `sourmash`: > ```python > import micropip > await...

upgrade plugin documentation

3

Dev docs: https://sourmash.readthedocs.io/en/latest/dev_plugins.html - * suggest adding plugins to https://github.com/ctb/sourmash-mixers * suggest plugins be added whenever new dependencies would be needed CLI docs: https://sourmash.readthedocs.io/en/latest/command-line.html#using-sourmash-plugins - * link to sourmash-mixers together...

if we deprecate a plugin, is it sensible to release a version of the plugin that removes the entry point?

1

for example, the latest version of [betterplot](https://github.com/sourmash-bio/sourmash_plugin_betterplot/?tab=readme-ov-file#venn---plot-2--or-3-way-sketch-intersections-using-venn-diagrams) contains the [venn plugin](https://github.com/sourmash-bio/sourmash_plugin_venn) functionality. should I release a new version of venn that removes that entry point? (and indicates that it's deprecated...

ref https://github.com/sourmash-bio/sourmash/issues/3095#issuecomment-2226993974 - I have a niggling worry that we are not properly distinguishing queries based on md5.

for internal sigs? https://www.baeldung.com/linux/xz-compression Used by AllTheBacteria as well.

2024 STAMPS tutorials - "running k-mer analyses with sourmash" venn & upset diagrams, ordination, and presence/absence diagram

3

https://hackmd.io/9ORFRJGaTOiOdEAY-Aih2A?view --- # open lab / Sat + Monday , Jul 20 & 22, 2024 / STAMPS 2024 Suggestion for open lab: * run the commands below on the "canned"...

(This is intended to be a long-running infodump. Please suggest additions or amendments in comments!!) sourmash branchwater provides real-time search of the Sequence Read Archive metagenomes along with a map...

more items to address

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after #313 - [ ] upgrade summarize with weighted! - [ ] adjust config file(s) for removed flags / issue warnings - [ ] detect non-paired-end??