Jim Shaw

jimshaw.bsky.social

14 October 2026 06:25

Skani (github.com/bluenote-157...) is now v0.4.0! Big performance update: **~2.5x faster** and ~30-40% less RAM for average nucleotide identity (ANI) comparison of genomes. The database format has changed (breaks forward compatibility; watch out!).

Camille Marchet ⚡

camillemrcht.bsky.social

12 October 2026 20:49

I tried to cook mac&cheese several times. Consistently failed. Thought it was French DNA preventing a catastrophe. Turns out, it was not. The key ingredient, my friends, is Maroilles!

Rob Patro

robp.bsky.social

26 September 2026 11:05

Cuttlefish 3.0.3 is out! github.com/COMBINE-lab/... Fun little jaunt with Opus 5.5 to substantially reduce the memory requirement (especially at moderate thread counts). Now it's both non-trivially faster *and* more memory-frugal than the initial C++ implementation!

Rob Patro

robp.bsky.social

17 September 2026 19:54

Our bramble preprint is out. Here's a thread about this work and why I think it's exciting! bsky.app/profile/robp...

Rob Patro

robp.bsky.social

03 September 2026 21:51

Something I've been thinking about for a while; with raw FASTQ files at one extreme & count matrices on the other, what's is the "right" archival/transfer format for scRNA-seq data? Big question but big potential "unlocks". Preprint soon (I hope), but here's a sneak peek :): crates.io/crates/gravlax