We built fgbio years ago to support UMI-aware sequencing.
As datasets grew, the single-threaded design started to show its limits.
fgumi is the next iteration: same expected outputs, rewritten for performance and scale.
github.com/fulcrumgenom...
Blog post details below👇
Question for the rust-bio folks: any recommendations on a dynamic de-bruijn graph crate?
I found some DBG crates but they seem to be A) unmaintained and/or B) not for dynamic applications.
The new syntax parser highlights exactly where in the code a compilation error is
Finally, some better syntax parsing in Nextflow! seqera.io/blog/nextflo...
Finally got around to fixing the main limitation of the current vcfdist release: exploding memory usage and runtime in regions with high-density variants. A new `--max-supercluster-size` parameter limits this. Release v2.6.0 is out on [Github](github.com/timd1/vcfdist), DockerHub, and bioconda!
Schematic figures showing global pairwise alignment algorithms
A worked example for each algorithm
Schemetic figures showing various modes, such as semi-global, local, and extension alignment
New set of thesis figures on pairwise alignment just dropped!
- schematic and worked example for many algorithms
- alignment modes
Graph between 1/20 and 2/28 of fiscal year 2024 and 2025 new awards in the EDU directorate.
🧪🚨 NSF's Directorate for STEM Education (EDU) has halted making nearly all new awards since inauguration day.
Among *many* other things, EDU runs the Graduate Research Fellowship Program (GRFP).
We need to protect the education & training of the next gen of scientists #StandUpForScience
Thread👇🧵
openRxiv has arrived!
We’re thrilled to announce the launch of openRxiv as an independent, researcher-led nonprofit to oversee bioRxiv and medRxiv, the world’s leading preprint servers for life and health sciences.
openrxiv.org/introducing-...
#openRxiv #OpenScience #Preprints #bioRxiv #medRxiv
Roche's SBX sequencing by expansion - preprint out!
www.biorxiv.org/content/10.1...
Another assault on US competitiveness at a time when biomedicine is roaring with innovation, an own-goal in a high-stakes international tournament. Of course the real losers are American people needing medicines and cures.
www.washingtonpost.com/health/2025/...
'Almost all of these actions are illegal, and many are actually unconstitutional. The administration is obviously daring someone to try to stop them, and as mentioned in Part Six below, right now that's the Federal Judiciary.'
www.science.org/content/blog...
Finally took the time to migrate from Twitter/X over to BlueSky!