downloading & sketching genomes by NCBI taxonomic hierarchy

[ctb]

here is code that uses the NCBI REST API to grab genome links and produce directsketch-compatible input CSVs for sketching:

https://github.com/ctb/2025-ncbi-rest-api

Related issues:

• are there instructions anywhere for using directsketch to sketch all reference genomes under a certain taxonomic node? sourmash_plugin_directsketch#166
• classify plant reads in metagenomes #3172

[ctb]

note also that that repo contains scripts for comparing directsketch input CSVs/ ("links CSVs") and sketch databases, and outputting the differences; as well as subtracting links CSVs. So we can sketch only things that haven't already been sketched, and build subtree tax databases like "all euks, minus metazoa and fungi and plants".

[ctb]

closing in favor of #3504, which has files, instructions for using them, and links to relevant repos 🎉