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do a contamination analysis on AllTheBacteria?

per https://github.com/AllTheBacteria/AllTheBacteria/issues/28

tutorial: combine results from multiple `fastgather` database searches using picklists

https://hackmd.io/ph9Q4nGHTb6T1mVJSV5yqw?view ref https://github.com/sourmash-bio/sourmash/issues/3233#issuecomment-2203433558, cc @musquita - # combining results from multiple different gathers Suppose you are using `fastgather`, and you want to combine the results from searching against multiple zip...

ctb

containment search tutorial: searching for genomes in metagenomes

https://hackmd.io/tKpLr1ISR9mqHHmZbEvcow?view # containment search tutorial: mgmanysearch ## Install relevant sourmash stuff ``` mamba create -y -n contain_tut sourmash_plugin_branchwater mamba activate contain_tut pip install sourmash_plugin_containment_search ``` ## Get data Download 2.2...

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tutorial

explore extending branchwater plugin to load zip files for prefetch and gather, entirely on rust side?

this could be a good & substantive next step towards higher-level oxidation of sourmash internals - what if we added a `load_from` plugin entry point to branchwater that loaded zip...

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[pre-commit.ci] pre-commit autoupdate

updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.10 → v0.5.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.10...v0.5.0)

pre-commit-ci[bot]

Enable codspeed

Saw this in North Bay Python 2024, seems like a great complement (or replacement?) for `asv`

luizirber

add gather implementation benchmarks to sourmash docs

hackmd: [link](https://hackmd.io/EoYofvlFQ0SPF3wANO2w7Q?both) # gather benchmarking - sourmash v4.8.10 / branchwater plugin v0.9.5 Source repo: [sourmash-bio/2024-benchmark-gather](https://github.com/sourmash-bio/2024-benchmark-gather) ## sample SRR1976948 This sample contains 177 genomes. Benchmarking results with 64 threads (note pygather...

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