C. Titus Brown
C. Titus Brown
I think it might be time to push forward with a release for spacegraphcats v3, which would break all our old results and workflows a bit ;). motivating PRs -...
in talking with @hehouts @ccbaumler I made the bold statement that: if you extracted a neighborhood from a catlas with r=10, then the neighborhood for r=9 would be contained within...
https://github.com/dib-lab/2020-ibd/blob/master/scripts/sig_to_csv.py perhaps do this for import too?
This came up on microbial bioinformatics slack, thought I'd share - topic was selecting from many viral genomes. > it should be possible to use large-scale ANI-style analyses to select...
This PR adds a `tax summarize` command per #2212. It also: * tackles native loading of with-lineages files produced by `tax annotate` as taxonomy spreadsheets (not yet implemented) * improves...
these have accumulated over time with recent wild proliferation... which ones am I missing? 😠## actual core repos - https://github.com/sourmash-bio/sra_search - actual `searcher` code in Rust - https://github.com/sourmash-bio/wort -...
In #2321 and https://github.com/sourmash-bio/sourmash/pull/2322 we delve back into multigather... and I remembered how annoying the CSV output is, in that it is output to the signature `filename` for each query....
luiz's talk about how we develop/design/evolve sourmash: https://www.youtube.com/watch?v=0jpnP8NtRfc&feature=youtu.be
This is a summarization of remaining issues in #838, which has become unreadable :) ---- from @luizirber in https://github.com/dib-lab/sourmash/issues/838#issuecomment-573856948: I'll dump here some other pointers to `gather` improvements, and they...
I'm on day 3 of a gather of the Hu S1 dataset against all genbank (500k+ genomes), and chatting with @taylorreiter about the find-the-unassigned script that @luizirber wrote, https://github.com/taylorreiter/cosmo-kmers/blob/master/scripts/unassigned.py it...