Phil Ewels23h ago

Super excited to be launching two things today: #RustQC 🦀🧬 and rewrites.bio 🚀

I used AI to rewrite 15 RNA-seq QC tools into a single Rust binary (I've never written any Rust). It ended up being over 60x faster. Here's the story 🧵

https://seqeralabs.github.io/RustQC/

Welcome to RustQC

Fast quality control tools for sequencing data, written in Rust.

RustQC
Show threadPhil Ewels23h ago

dupRadar keeps breaking @nf_core #rnaseq runs. So as a bit of a joke, I prompted #Claude Code + Seqera AI to rewrite it in Rust. My Slack message:

"I did a rust rewrite over lunch. I realize that I might have accidentally also made a super fast Rust implementation of featureCounts."

Show threadPhil Ewels23h ago

By the end of the weekend I had replaced all 15 QC tools in nf-core/rnaseq: dupRadar, featureCounts, RSeQC, preseq, samtools stats, Qualimap.

RustQC produced all outputs with a single read of the BAM file. Time went from 15 hours to 15 minutes, >60x faster.

Suddenly this wasn't a joke any more!

Show threadPhil Ewels23h ago

#RustQC is a drop-in replacement - the output files are near-identical to the originals, so @multiqc works out of the box.

I wrote a blog post about this story, so you can read in a bit more detail here:

https://seqera.io/blog/rustqc

Introducing RustQC: 15 RNA-Seq QC Tools in One Pass, Built with AI | Seqera

RustQC is a Rust reimplementation of 15 RNA-seq QC tools consolidated into a single binary. One pass through the BAM file gives functionally identical outputs, but with >60x faster run time and drastically reduced I/O.

Show threadPhil Ewels23h ago

I'm not unique in getting here. 3 days into my effort, @rob wrote about using AI to rewrite piscem (https://combine-lab.github.io/blog/2026/02/15/a-skeptics-guide-to-generative-ai-coding.html). Then
Fulcrum Genomics released #fgumi this week (https://blog.fulcrumgenomics.com/p/introducing-fgumi).

Something has clearly shifted in AI capabilities..

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Show threadPhil Ewels

I'm both excited and a little terrified. It feels like a wave of AI-assisted tool rewrites is coming to bioinformatics whether we like it or not.

We figured that the best we can do is to try to get ahead of it, so we wrote down some principles for doing it responsibly:

https://rewrites.bio

rewrites.bio - A manifesto for bioinformatics

Principles for responsible AI-assisted rewriting of bioinformatics tools.

rewrites.bio
Apr 2 at 4:05pmWeb
Show threadPhil Ewels23h ago

rewrites.bio is all pretty common sense stuff: credit original authors, emulate output exactly, maintain what you ship, don't spam open-source maintainers with AI-generated bug reports.

I wrote a second blog post covering this part of the story here:

https://seqera.io/blog/rewrites-bio/

rewrites.bio: Principles for AI-assisted Modernization of Scientific Software | Seqera

A wave of AI-driven tool rewrites is coming to bioinformatics. We've published a set of best-practices principles to try to help people to approach rewrites in the right way.

Show threadPhil Ewels23h ago

Writing code is cheap now, but the scientific insight and community trust behind the tools being rewritten hasn't changed. I'm feeling cautiously optimistic.

→ RustQC: https://seqeralabs.github.io/RustQC/
→ rewrites.bio: https://rewrites.bio

→ RustQC blog: https://seqera.io/blog/rustqc
→ rewrites blog: https://seqera.io/blog/rewrites-bio/

Welcome to RustQC

Fast quality control tools for sequencing data, written in Rust.

RustQC