C. Titus Brown

Update README.rst

1

I think this is correct?

e.g. some of the Mouse refseq sequences ## Problem Description ## My Environment ### Operating System ### Python Environment ### LAST Version ### Shmlast Output

## Problem Description ## My Environment ### Operating System ### Python Environment ### LAST Version ### Shmlast Output

A quickstart running on Mac OS X

10

Bits and pieces of comparem are mildly incompatible with Mac OS X (Sierra, in my case). See [this quickstart](https://hackmd.io/EwMwbAnGCsAs0Fp4GYRIIYCNERMZCAHMhMQOwCmm6hAxgCZA?view) for getting it working. I'll provide patches and pull requests as...

is full `snakemake` required? or would `snakemake-minimal` suffice?

2

I noticed in your `environment.yml` file you install snakemake - curious about whether you need full `snakemake` or if `snakemake-minimal` would be sufficient. The advantage is that minimal is much...

Include preprints

8

Preprinting (as opposed to open access, #9) seems like an omission from the current topic suggestions.

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

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...

containment search tutorial: searching for genomes in metagenomes

1

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...

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

1

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...