sourmash

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asked on slack by Jonathan Rondeau-Leclaire - >I am trying to understand the scaled argument in sourmash gather. Can you point me to what I need to read to understand...

ctb

suggestions for mastiff

3

A few thoughts on mastiff/SRA-search-as-a-service moving forward - * we are likely to want to provide multiple databases / versions of databases down the road - in particular, real-time search...

ctb

Bump finch from 0.4.1 to 0.4.3

1

Bumps [finch](https://github.com/onecodex/finch-rs) from 0.4.1 to 0.4.3. Release notes Sourced from finch's releases. Version 0.4.3 Minor release that includes new no_strict=False parameter in sketch_file() Python binding. Version 0.4.2 This is a...

dependabot[bot]

[WIP] begin adding the machinery for CSV column renaming

1

Tackling https://github.com/sourmash-bio/sourmash/issues/1555 TODO: - [ ] provide column documentation for v5

ctb

I asked: >If I'm digging into performance issues in Python code (e.g. sourmash), what profiler(s) should I be using? thx! Luiz answered: >My default rec is py-spy and heaptrack: https://blog.luizirber.org/2020/01/10/sourmash-pr/...

ctb

conda install problem w/python3.10: `libffi.so.7: cannot open shared object file: No such file or directory`

3

Can't wait to try the new version! ``` $ mamba install sourmash # v4.5.0 $ sourmash -v Traceback (most recent call last): File "/home/shenwei/app/miniconda3/envs/kmcp/bin/sourmash", line 7, in from sourmash.__main__ import...

shenwei356

can we update clustering results with new signatures?

3

we're starting to develop more options for large-scale clustering of sketches over in https://github.com/sourmash-bio/sourmash/issues/2271 (GTDB and SRA scale, even!). one feature that's been requested and discussed in the [µbioinfo slack](https://microbial-bioinfo.slack.com)...

ctb

per conversation with @bluegenes, our similarity, avg, and max-containment based ANI values are symmetric, which seems like a strong advantage for matrix generation and analysis. this is not true for...

ctb

fast clustering of many large sketches - kspider

1

@mr-eyes has been working steadily on using kspider ([docs](https://dib-lab.github.io/kSpider/) and [repo](https://github.com/dib-lab/kspider)) to cluster many large collections of k-mers, and has achieved some impressive results. This issue is b/c I wanted...

ctb

release process updates for release after v4.5.0

1

(presumably v4.5.1 ;)) when releasing [v4.5.0](https://github.com/sourmash-bio/sourmash/issues/2241), I ran into a few problems - * it would be good to put the post-release checklist further up in the how-to-release doc *...

ctb