Seth Stadick

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.

The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...

Figure 1 shows they key result

The ergonomics of this are beautiful.

The Quickening In a paper titled “THEOREMS FOR A PRICE: Tomorrow’s Semi-Rigorous Mathematics Culture” published in 1993, mathematician Doron Zeilberger wrote: There are writings on the wall that…

Some thoughts on AI based on working on this project: Some thoughts on AI based on working on this project: liorpachter.wordpress.com/2026/02/19/t...

We are excited to announce that we can successfully use Rust's async/await on the GPU. This has never been done before.

www.vectorware.com/blog/async-a...

Supporting Rust's async/await (and futures) enables existing Rust code to work on the GPU and makes GPU programming more ergonomic.

COMBINE-lab - The skeptic’s guide to generative AI assisted coding An easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more.

I’ve written a post about my recent experiences (successes) with AI coding models; the experiences that caused me to re-evaluate my initial judgements, the surprise I had at what can be accomplished, & some fears I have about these tools. Discussion welcome! combine-lab.github.io/blog/2026/02...

setting on github to set commit message of a squashed PR to PR title + description

TIL this setting on GitHub. kinda mad about the years of git commits could have contained my beautiful PR descriptions

ziglang.org/devlog/2026/...

> it seems we are indeed reaching the Promised Land, where Zig code can have Io implementations effortlessly swapped out

hat: a cargo-like wrapper around pixi for managing mojo projects.

github.com/sstadick/hat

It literally just shells out to pixi and is meant to be very transparent! 100% compatible with pixi.

And to counter the slightly anti-ai stance in the essay, here's pretty pro-ai take that seems like a really nice balanced usage model:

mitchellh.com/writing/my-a...

This essay keeps feeling more salient the more I work with various AI agents.

That's not to say that agents aren't massive enablers in some cases. There's just tradeoffs.

So anyway:
BiRank & QuadRank: single-cache-miss rank queries that are double the throughput of other Rust crates and fully saturate the memory bandwidth.
Side effect: QuadFm is smaller and 2-4x faster than the next-best FM-index.

github.com/RagnarGrootK...

raw.githubusercontent.com/RagnarGrootK...

I've just released #rust-htslib 1.0. After a long time with a pretty stable API usage of rust-htslib in production, it feels like the right time to finally move to 1.0. Most important change is probably a switch to thread-safe pointers in BAM record handling. github.com/rust-bio/rus...

I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!

I am hiring a staff bioinformatician for my new lab at the University of Utah! Please consider applying if you are on the hunt:
employment.utah.edu/salt-lake-ci...

We ❤️ our users in academia – and we love to read their success stories.

PS: If you think your institute/company could benefit from Pixi as well, and you want to learn more, please reach out to us to plan something! We're looking forward to organize more workshops this year.

There’s dozens of us!

I use it in place of both Rust and Python! 2026 should be the year they open source the compiler.

Advent of Code Day 12:

codeberg.org/sstadick/aoc...

Screenshot of SAM spec for the SEQ field that says a single `*` is valid when the sequence is not stored.

TIL that a single `*` is a valid SEQ in SAM spec.

It makes sense in retrospect, but I did not cover that edge case.
github.com/sstadick/per...

feat: day11 part a and b M3 Air Part A: ```bash ❯ hyperfine --warmup 3 ./main Benchmark 1: ./main Time (mean ± σ): 6.3 ms ± 3.7 ms [User: 4.4 ms, System: 1.6 ms] Range (min … max): 4.3 ms … 49.8 ms 39...

Advent of Code Day 11:

codeberg.org/sstadick/aoc...

day10: there was an attempt Part a solved, Part b heat death of the universe.

Advent of Code Day 10: codeberg.org/sstadick/aoc...

The wall has been hit on part 2. I know what it is I don't know... I just need a few days to re-learn the math.

@typst.app really is as good as the hype.

It’s hard to recommend till it’s truly open source, but there’s a lot to like for sure!

With @Modular looking to hit Mojo 1.0 and open source the Mojo compiler in 2026, I strongly suspect we'll see a huge uptick in Mojo usage in bioinformatics and data science next year.

Not the first paper I've been a part of, but the first one I've ever written, organized, and executed! I learned a lot getting this one done.

Also, Mojo! 🔥 👇

feat: day9 part 1 and part 2 M3 Spent a long time on part B. First try was to check every point on the boundary of the rectangle to see if it was inside the polygon by raycasting. That worked but was very slow and didn't scale u...

Advent of Code Day 9:
codeberg.org/sstadick/aoc...

Classic part B where I thought I had it solved.... and then two hours later figure out the trick.

🧬Explore the latest from Bioinformatics Advances: “Ish: SIMD and GPU accelerated local and semi-global alignment as a CLI filtering tool.”  

Read the full paper here: https://doi.org/10.1093/bioadv/vbaf292

Author: @ducktapeprogrammer.bsky.social

Advent of Code Day 8: codeberg.org/sstadick/aoc...

Time to go read up on the correct way to solve this one.

feat: day7 part a and b M3 Part A ```bash ❯ hyperfine --warmup 3 ./main Benchmark 1: ./main Time (mean ± σ): 3.7 ms ± 0.3 ms [User: 2.9 ms, System: 0.8 ms] Range (min … max): 3.3 ms … 4.7 ms 517 ru...

Advent of Code Day 6:

codeberg.org/sstadick/aoc...

feat: day6 part 1 and 2 Nothing elegant in my solution for today. Part 1: ```bash ❯ hyperfine --warmup 3 ./main Benchmark 1: ./main Time (mean ± σ): 4.0 ms ± 0.3 ms [User: 3.5 ms, System: 0.9 ms] Range (min ...

Advent of Code day6!

Nothing elegant about my approach today, just a "get it done before the kids wake up" solution.