C. Titus Brown
C. Titus Brown
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...
Tackling https://github.com/sourmash-bio/sourmash/issues/1555 TODO: - [ ] provide column documentation for v5
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/...
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)...
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...
@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...
(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 *...
prefetch and gather use different CSV column headers for their output, and I'm sure so does search and other commands. Would be good to fix this in v5.
This PR adds support for direct loading of signatures via HTTP URLs with `GET`, i.e the normal way of getting files from a Web server. See discussion here, https://github.com/sourmash-bio/sourmash/issues/2257. **NEXT...
over in https://github.com/sourmash-bio/sourmash/pull/2256, I have an experimental PR that adds direct loading of .sig files (JSON format) via HTTP GET, using the `requests` library. It's remarkably simple and it provides...