C. Titus Brown

https://link.springer.com/article/10.1186/s13015-025-00276-8

eukaryotic genome databases are now available on farm as well as for download 🎉 . These databases contain (almost) every reference genome under [NCBI taxonomy node 2759](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2759&lvl=3&lin=f&keep=1&srchmode=1&unlock) - a total...

A variety of different copies of this script are now floating around... This one is the latest (as of jan 25, 2025) - https://github.com/sourmash-bio/2025-sourmash-ncbi-viral-databases/blob/main/scripts/taxid-to-lineages.taxonkit.py

viral genome databases are now available on farm as well as for download! 🎉 TODO: - [ ] add them to the databases page ## files location: `/group/ctbrowngrp5/sourmash-db/ncbi-viruses-2025.01` The .sig.zip...

proper compilation of `lib_lowlevel` is confusing

1

I've been having trouble with developing FFI methods, and I think I figured out at least one of the problems (although I am not sure where to go for the...

use `MemRevIndex`-based `CounterGather` for Python index classes?

1

https://github.com/sourmash-bio/sourmash/pull/3545 implements a full memory-based `RevIndex` and also provides a `CounterGather` class that might be useful for gather. Maybe we should consider replacing the current Python-based `CounterGather` implementation? The following...

GTDB rs226 databases now available!

6

see: https://github.com/sourmash-bio/sourmash_plugin_directsketch/issues/254

`match_name` vs `name` problems... did we fix this?

update branchwater plugin documentation to mention that sourmash v4.9.0 natively supports rocksdb

1

added in https://github.com/sourmash-bio/sourmash/pull/3545

refactor `lib.kmerminhash_angular_similarity` (Rust/FFI)

1

https://github.com/sourmash-bio/sourmash/pull/3644 removes use of this function because it doesn't downsample. Evaluate for fixing or removal.