C. Titus Brown

summary: selectors are good, let's maybe have more of them.

2

This is an update of & replacement for https://github.com/dib-lab/sourmash/issues/1072, which introduced the idea of a `database.select(...)` function. This issue is being updated after the release of sourmash 4.1. --- In...

document that files in pathlists are relative to the cwd, not to the pathlist location.

2

currently, the file list returned by `load_file_list_of_signatures` is assumed to be relative to current working directory; an equally natural behavior would be to load relative paths based on the dirpath...

explain p_match and p_query in sourmash documentation

8

it's not easy to find!

add more documentation about what gather does, and what the fields are.

2

as we explore the min-set-cov analysis, we're coming up with some interesting viz, e.g. #1225, and adding new output fields #1219. I think Appendix A, [How sourmash gather works](https://sourmash.readthedocs.io/en/latest/classifying-signatures.html#appendix-a-how-sourmash-gather-works), could...

use cases

9

This issue can serve as a placeholder for use cases for sourmash/MinHash more generally. Stuff we already have implemented: * basic MinHash comparisons etc * metagenome taxonomy breakdown * streaming...

provide a way to calculate _differences_ in taxonomic classification for samples

4

provide a way to calculate differences in taxonomic classification for samples. ref #367

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describe sourmash estimates and their correlations with read mapping rates

2

documentation updates needed: we now have a lot of good evidence that f_match correlates with the fraction of genome that will be covered by mapped reads, per the [sourmash gather/minimum...

consider adjusting search `--threshold` default value and how `-n` works

3

see https://github.com/sourmash-bio/sourmash/issues/2168 - a few ideas: * remove `-n` completely, 'cause it's a bit silly; * increase `-n` to be something larger than three; * adjust docstring for `-n` to...

sourmash repositories on github

1

This is a list of repositories for sourmash, software for rapidly searching and analyzing genomes and metagenomes! The main repository - [sourmash-bio/sourmash](https://github.com/sourmash-bio/sourmash/) - please file all questions and issues here!...