2024 package contributions to enable short-sequence viral taxonomy
===

## branchwater
- [branchwater #134](https://github.com/sourmash-bio/sourmash_plugin_branchwater/pull/134)
- (the largest one!) [branchwater #197](https://github.com/sourmash-bio/sourmash_plugin_branchwater/pull/197/)

nearly finished:
- [branchwater #205](https://github.com/sourmash-bio/sourmash_plugin_branchwater/pull/205)
- [branchwater #217](https://github.com/sourmash-bio/sourmash_plugin_branchwater/pull/217)

## sourmash

- [sourmash #2948](https://github.com/sourmash-bio/sourmash/pull/2948)
- [sourmash #2986](https://github.com/sourmash-bio/sourmash/pull/2986)
- [sourmash #2931](https://github.com/sourmash-bio/sourmash/pull/2931)
- [sourmash #2608](https://github.com/sourmash-bio/sourmash/pull/2608)

nearly finished:
- [sourmash #2943](https://github.com/sourmash-bio/sourmash/pull/2943)
- [sourmash #3007](https://github.com/sourmash-bio/sourmash/pull/3007)

Working code in the process of testing:

- [rustworkx clustering code](https://github.com/bluegenes/2023-spillover-smash/blob/main/pairwise-to-clusters-rustworkx.py)

# benchmarks feb 2024

| software/version | command | details | time | max RAM |
| -------- | -------- | -------- | -- | -- |
| sourmash v4.8.6 | `gather` | the OG | 42m 26s | 14.5 GB |
| branchwater v0.9.0-pre | `fastgather` | against zip | 2m 5s | <span style="color:red">**14.1 GB**</span> |
| branchwater v0.0.9-pre | `fastgather` | against pathlist | <span style="color:darkred">**36m 4s**</span> | 1.9 GB |
| branchwater v0.9.0-pre | `fastmultigather` | against rocksdb | 2m 8s | <span style="color:green">**600 MB**</span> |

full version: https://github.com/sourmash-bio/sourmash_plugin_branchwater/issues/214