Tim Dunn

A CRISPR off-target search cannot report a sequence it was never given. @ameynert.bsky.social explains how DivRef brings common human variants and haplotypes into the search space—and how her rebuild complements @timd.one work on Sassy. Read Alison’s post: blog.fulcrumgenomics.com/p/a-crispr-o...

CRISPR off-target search can find the right locus while hiding plausible alignments within it. I wrote about how Sassy v0.2.5 uses recursive backtracking to report every reasonable alignment—more than 9× as many in under 30 seconds. blog.fulcrumgenomics.com/p/why-crispr...

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.

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!

New set of thesis figures on pairwise alignment just dropped! - schematic and worked example for many algorithms - alignment modes

🧪🚨 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...

'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!