#Snakemake 9.23 has been released. It adds the ability to use gh/gl shorthands for specifying source files (e.g. Snakefiles) from Github oder Gitlab repositories. In addition, source retrieval from Github/Gitlab has been optimized and further secured. snakemake.github.io
Another #Snakemake release (9.22.0). We have added a new default pathvar, new semantic helpers for choosing directories or files from alternatives, extended provenance information and Python 3.14 support. In addition various bugs have been fixed. snakemake.github.io
#rustbio 4.0 has been released. It harmonizes the error handling, improves the API, makes gap-open/extend behavior in pairwise alignment more intuitive and in-line with the literature, improves GFF parsing, and allows incremental building of the rank-select datastructure. github.com/rust-bio/rus...
Johannes Köster
Johannes Köster
Johannes Köster
It’s amazing how quickly we lose fluency in languages we don’t use frequently. I think many coders are going to find out the hard way that we don’t call programming languages that just for convenience.
All to say I like this idea and will likely try the same (outside existing build-AI-to projects.)
I'm going to try something next month. AI deskilling is real. I'm going a month without it. blog.stephenturner.us/p/ai-dry-july
Introducing nail - a Rust implementation of profile HMM sequence alignment for proteins. Near-HMMER sensitivity, but a lot faster:
www.biorxiv.org/content/10.1...
github.com/TravisWheele...
Congrats to @leoackermann.bsky.social on winning RECOMB's best poster award for his work on compressing pairwise distance matrices!
Check it out here: lacker.gitlab.io/pdf/research...
Dr. Stephanie
www.biorxiv.org
lacker.gitlab.io
Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. www.biorxiv.org/content/10.6...
