building large LCA databases for genbank subsets

[ctb]

from #462 (comment), @J-I-P says:

OK, I try to build a LCA database ( only bacteria in NCBI) now. I want to use this database to sourmash lca summarize or sourmash lca classify my zymo data.

and I wanted to continue that conversation in a new issue. here we are! my response below:

cool - we have various LCA databases already available here, but started running into scalability challenges as the number of microbial genomes in genbank increased to over 500,000!

we've been working on resolving those scalability issues as well as changing the way we handle taxonomy to better support various approaches.

some links you might find interesting -

• how the lineage spreadsheet works (for lca index) How do I build a lineage spreadsheet for GTDB taxonomy and signatures? #1095
• techniques for downloading stuff from NCBI in bulk Building genbank/refseq databases from assembly_summary.txt databases#7
• using GTDB taxonomy instead of NCBI taxonomy tracking gtdb databases #802, and GTDB databases available add GTDB databases to docs #816

[ctb]

This is now easy to do with picklists and taxonomies; closing for now.