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 🧵
seqeralabs.github.io/RustQC/
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 🧵
seqeralabs.github.io/RustQC/
Welcome to RustQC
Fast quality control tools for sequencing data, written in Rust.
seqeralabs.github.io
April 2, 2026 at 3:51 PM
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 🧵
seqeralabs.github.io/RustQC/
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 🧵
seqeralabs.github.io/RustQC/
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: seqeralabs.github.io/RustQC/
→ rewrites.bio
→ RustQC blog: seqera.io/blog/rustqc
→ rewrites blog: seqera.io/blog/rewrite...
→ RustQC: seqeralabs.github.io/RustQC/
→ rewrites.bio
→ RustQC blog: seqera.io/blog/rustqc
→ rewrites blog: seqera.io/blog/rewrite...
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 drasti...
seqera.io
April 2, 2026 at 3:51 PM
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: seqeralabs.github.io/RustQC/
→ rewrites.bio
→ RustQC blog: seqera.io/blog/rustqc
→ rewrites blog: seqera.io/blog/rewrite...
→ RustQC: seqeralabs.github.io/RustQC/
→ rewrites.bio
→ RustQC blog: seqera.io/blog/rustqc
→ rewrites blog: seqera.io/blog/rewrite...
My talk from the #NextflowSummit is on YouTube! youtu.be/LbA_d4oOpDQ
I talked about my recent odyssey with AI-written software, including #RustQC, rewrites.bio, Trim Galore and a FastQC rust rewrite 👀
This was honestly one of my favourite talks to date. I hope it's interesting for folks 😊
I talked about my recent odyssey with AI-written software, including #RustQC, rewrites.bio, Trim Galore and a FastQC rust rewrite 👀
This was honestly one of my favourite talks to date. I hope it's interesting for folks 😊
Phil Ewels: Bioinformatics in the agentic age: Practical tips learnt from RustQC and rewrites.bio
YouTube video by Nextflow
youtu.be
May 13, 2026 at 9:55 PM
My talk from the #NextflowSummit is on YouTube! youtu.be/LbA_d4oOpDQ
I talked about my recent odyssey with AI-written software, including #RustQC, rewrites.bio, Trim Galore and a FastQC rust rewrite 👀
This was honestly one of my favourite talks to date. I hope it's interesting for folks 😊
I talked about my recent odyssey with AI-written software, including #RustQC, rewrites.bio, Trim Galore and a FastQC rust rewrite 👀
This was honestly one of my favourite talks to date. I hope it's interesting for folks 😊
RastQC: High-Performance Sequencing Quality Control Written in Rust https://www.biorxiv.org/content/10.64898/2026.03.31.715630v1
April 2, 2026 at 10:33 PM
Introducing RustQC: 60x faster RNA-Seq quality control!
We used AI to reimplement 15 RNA-Seq QC tools (dupRadar, Qualimap, RSeQC, Preseq, samtools, featureCounts) into a single tool, written in @rust-lang.org:
✅ 15 h analyses → 15 min
✅ Identical outputs
✅ Drastically reduced I/O
We used AI to reimplement 15 RNA-Seq QC tools (dupRadar, Qualimap, RSeQC, Preseq, samtools, featureCounts) into a single tool, written in @rust-lang.org:
✅ 15 h analyses → 15 min
✅ Identical outputs
✅ Drastically reduced I/O
April 2, 2026 at 3:38 PM
Introducing RustQC: 60x faster RNA-Seq quality control!
We used AI to reimplement 15 RNA-Seq QC tools (dupRadar, Qualimap, RSeQC, Preseq, samtools, featureCounts) into a single tool, written in @rust-lang.org:
✅ 15 h analyses → 15 min
✅ Identical outputs
✅ Drastically reduced I/O
We used AI to reimplement 15 RNA-Seq QC tools (dupRadar, Qualimap, RSeQC, Preseq, samtools, featureCounts) into a single tool, written in @rust-lang.org:
✅ 15 h analyses → 15 min
✅ Identical outputs
✅ Drastically reduced I/O
#RustQC is a drop-in replacement - the output files are near-identical to the originals, so @multiqc.info works out of the box.
I wrote a blog post about this story, so you can read in a bit more detail here: seqera.io/blog/rustqc
I wrote a blog post about this story, so you can read in a bit more detail here: 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 drasti...
seqera.io
April 2, 2026 at 3:51 PM
#RustQC is a drop-in replacement - the output files are near-identical to the originals, so @multiqc.info works out of the box.
I wrote a blog post about this story, so you can read in a bit more detail here: seqera.io/blog/rustqc
I wrote a blog post about this story, so you can read in a bit more detail here: seqera.io/blog/rustqc
Agreed, to a degree - see a similar discussion on a thread in the Nextflow slack. Note that I did make extensive use of rust-htslib in RustQC. I think that there are diminishing returns the closer you get to a final result though.
That said, if RustQC can provide a library then shout, happy to try!
That said, if RustQC can provide a library then shout, happy to try!
April 2, 2026 at 9:39 PM
Agreed, to a degree - see a similar discussion on a thread in the Nextflow slack. Note that I did make extensive use of rust-htslib in RustQC. I think that there are diminishing returns the closer you get to a final result though.
That said, if RustQC can provide a library then shout, happy to try!
That said, if RustQC can provide a library then shout, happy to try!
I totally agree - the very first point on rewrites.bio is about academic integrity: "Credit the original authors".
I wasn't suggesting that rewrites should be published. People should cite the underlying tools, eg. seqeralabs.github.io/RustQC/about...
I wasn't suggesting that rewrites should be published. People should cite the underlying tools, eg. seqeralabs.github.io/RustQC/about...
Credits & Citation
Credits, citations, and acknowledgments for the tools and libraries that RustQC builds upon.
seqeralabs.github.io
April 7, 2026 at 6:55 AM
I totally agree - the very first point on rewrites.bio is about academic integrity: "Credit the original authors".
I wasn't suggesting that rewrites should be published. People should cite the underlying tools, eg. seqeralabs.github.io/RustQC/about...
I wasn't suggesting that rewrites should be published. People should cite the underlying tools, eg. seqeralabs.github.io/RustQC/about...
QC makes up half the runtime of a typical RNA-seq analysis. What if you could cut that down by 60x?⚡
RustQC consolidates 15 RNA-seq QC tools into a single Rust binary.🦀 One pass through the BAM file, with functionally identical outputs. >60x faster, with drastically reduced I/O. hubs.ly/Q04gY5MM0
RustQC consolidates 15 RNA-seq QC tools into a single Rust binary.🦀 One pass through the BAM file, with functionally identical outputs. >60x faster, with drastically reduced I/O. hubs.ly/Q04gY5MM0
Welcome to RustQC
Fast quality control tools for sequencing data, written in Rust.
hubs.ly
May 18, 2026 at 9:56 AM
QC makes up half the runtime of a typical RNA-seq analysis. What if you could cut that down by 60x?⚡
RustQC consolidates 15 RNA-seq QC tools into a single Rust binary.🦀 One pass through the BAM file, with functionally identical outputs. >60x faster, with drastically reduced I/O. hubs.ly/Q04gY5MM0
RustQC consolidates 15 RNA-seq QC tools into a single Rust binary.🦀 One pass through the BAM file, with functionally identical outputs. >60x faster, with drastically reduced I/O. hubs.ly/Q04gY5MM0
We're delighted to have contributed case studies to OpenAI's report on scientific computing in the age of agentic AI. 📃 hubs.la/Q04r75Zm0
Alongside Felix Krueger (Altos), we contributed agent-assisted rewrites of RNA-seq QC tools (RustQC, FastQC-Rust & more), built for @nextflow.io and @nf-co.re.
Alongside Felix Krueger (Altos), we contributed agent-assisted rewrites of RNA-seq QC tools (RustQC, FastQC-Rust & more), built for @nextflow.io and @nf-co.re.
Scientific computing in the age of agentic AI
A new field report shows how scientists use AI coding agents to modernize scientific computing, accelerating software development and discovery in genomics and beyond.
hubs.la
July 29, 2026 at 12:07 PM
We're delighted to have contributed case studies to OpenAI's report on scientific computing in the age of agentic AI. 📃 hubs.la/Q04r75Zm0
Alongside Felix Krueger (Altos), we contributed agent-assisted rewrites of RNA-seq QC tools (RustQC, FastQC-Rust & more), built for @nextflow.io and @nf-co.re.
Alongside Felix Krueger (Altos), we contributed agent-assisted rewrites of RNA-seq QC tools (RustQC, FastQC-Rust & more), built for @nextflow.io and @nf-co.re.
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!
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!
April 2, 2026 at 3:51 PM
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!
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!
Love it, thanks Phil! And huge props on both RustQC and rewrites.bio!
April 2, 2026 at 10:44 PM
Love it, thanks Phil! And huge props on both RustQC and rewrites.bio!
For pipelines processing thousands of samples, this means millions of CPU hours saved—with massive reductions in cost and carbon footprint.
💡Explore RustQC: seqera.io/blog/rustqc
💡Explore RustQC: 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 drasti...
seqera.io
April 2, 2026 at 3:38 PM
For pipelines processing thousands of samples, this means millions of CPU hours saved—with massive reductions in cost and carbon footprint.
💡Explore RustQC: seqera.io/blog/rustqc
💡Explore RustQC: seqera.io/blog/rustqc
Yeah I agree, this has always been the case but it's especially important now. I started with these 2 files and extended to a pipeline (github.com/seqeralabs/R...) and later the nf-core/rnaseq pipeline tests. There are a fair number of unit tests as well. Definitely could be improved though.
GitHub - seqeralabs/RustQC-benchmarks: Benchmark suite for validating RustQC outputs against upstream bioinformatics tools
Benchmark suite for validating RustQC outputs against upstream bioinformatics tools - seqeralabs/RustQC-benchmarks
github.com
April 10, 2026 at 9:53 PM
Yeah I agree, this has always been the case but it's especially important now. I started with these 2 files and extended to a pipeline (github.com/seqeralabs/R...) and later the nf-core/rnaseq pipeline tests. There are a fair number of unit tests as well. Definitely could be improved though.
We've applied these principles to RustQC, a Rust reimplementation of 15 RNA-seq QC tools that achieves a >60x speedup while producing identical output.
⚡Read the companion post for the full story of how it was built, the benchmarks, and what it means for Nextflow pipelines: hubs.la/Q04b85yT0
⚡Read the companion post for the full story of how it was built, the benchmarks, and what it means for Nextflow pipelines: hubs.la/Q04b85yT0
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.
hubs.la
April 9, 2026 at 9:16 AM
We've applied these principles to RustQC, a Rust reimplementation of 15 RNA-seq QC tools that achieves a >60x speedup while producing identical output.
⚡Read the companion post for the full story of how it was built, the benchmarks, and what it means for Nextflow pipelines: hubs.la/Q04b85yT0
⚡Read the companion post for the full story of how it was built, the benchmarks, and what it means for Nextflow pipelines: hubs.la/Q04b85yT0
Thanks! You mean on the RustQC homepage? Yes you're right, I should tweak that - a victim of trying to not get too into the weeds for a tagline, but I agree that it's a bit misleading.
Note that RustQC uses rust-htslib, so a lot of the underlying C code is likely the same as Samtools..
Note that RustQC uses rust-htslib, so a lot of the underlying C code is likely the same as Samtools..
April 2, 2026 at 6:51 PM
Thanks! You mean on the RustQC homepage? Yes you're right, I should tweak that - a victim of trying to not get too into the weeds for a tagline, but I agree that it's a bit misleading.
Note that RustQC uses rust-htslib, so a lot of the underlying C code is likely the same as Samtools..
Note that RustQC uses rust-htslib, so a lot of the underlying C code is likely the same as Samtools..
Yup, documentation of the validation is essential for user trust. I tried to be cautious with my language, differences in RustQC are typically at the 14th decimal place or similar. It's all detailed on the docs pages: seqeralabs.github.io/RustQC/rna/d...
It's also encoded in the CI snapshots.
It's also encoded in the CI snapshots.
dupRadar
RustQC's dupRadar output files, including the duplication matrix, fitted model parameters, diagnostic plots, and benchmark comparisons.
seqeralabs.github.io
April 10, 2026 at 11:03 AM
Yup, documentation of the validation is essential for user trust. I tried to be cautious with my language, differences in RustQC are typically at the 14th decimal place or similar. It's all detailed on the docs pages: seqeralabs.github.io/RustQC/rna/d...
It's also encoded in the CI snapshots.
It's also encoded in the CI snapshots.
Heng Li's blog posts are always thoughtful and well written, this is no exception.
Great to see folks coming to similar conclusions around #Rust #rewrites in bioinformatics.
Also appreciate the RustQC / rewrites.bio cite 🙏🏻
Great to see folks coming to similar conclusions around #Rust #rewrites in bioinformatics.
Also appreciate the RustQC / rewrites.bio cite 🙏🏻
Blog post on "The AI Rewrite Dilemma": lh3.github.io/2026/04/17/t...
The AI Rewrite Dilemma
lh3.github.io
April 18, 2026 at 5:54 AM
Heng Li's blog posts are always thoughtful and well written, this is no exception.
Great to see folks coming to similar conclusions around #Rust #rewrites in bioinformatics.
Also appreciate the RustQC / rewrites.bio cite 🙏🏻
Great to see folks coming to similar conclusions around #Rust #rewrites in bioinformatics.
Also appreciate the RustQC / rewrites.bio cite 🙏🏻
Now, I'm not saying that this setup can't work for something like RustQC. Such a tool might be easier to validate even if output isn't byte-for-byte identical. But that's not true for every bioinformatics tool out there.
April 10, 2026 at 6:22 AM
Now, I'm not saying that this setup can't work for something like RustQC. Such a tool might be easier to validate even if output isn't byte-for-byte identical. But that's not true for every bioinformatics tool out there.
@ewels.bsky.social from @seqera.io just dropped a mass of knowledge about RustQC, a single Rust binary replacing 15 RNA-seq QC tools with 60x faster speed, built entirely with AI and zero prior experience. Plus, rewrites.bio for responsible rewrite principles🤯 #NextflowSummit
April 30, 2026 at 3:11 PM
@ewels.bsky.social from @seqera.io just dropped a mass of knowledge about RustQC, a single Rust binary replacing 15 RNA-seq QC tools with 60x faster speed, built entirely with AI and zero prior experience. Plus, rewrites.bio for responsible rewrite principles🤯 #NextflowSummit
I'm not sure that such a thing is possible using LLMs trained on OSS code, to be honest. And for the most part I'm not sure I see the point either - I explicitly state that RustQC is not a clean room reimplementation. As long as everything is OSS hopefully there shouldn't be any issues.
April 3, 2026 at 5:12 AM
I'm not sure that such a thing is possible using LLMs trained on OSS code, to be honest. And for the most part I'm not sure I see the point either - I explicitly state that RustQC is not a clean room reimplementation. As long as everything is OSS hopefully there shouldn't be any issues.
You can find the PDF of the slides here: phil.ewels.co.uk/talks/2026/0...
Apologies for the dodgy audio on the recording! I tried fixing it but to no avail 🙈
Apologies for the dodgy audio on the recording! I tried fixing it but to no avail 🙈
Nextflow Summit 2026 - Boston | Phil Ewels
Bioinformatics in the agentic age: Practical tips learnt from RustQC and rewrites.bio
phil.ewels.co.uk
May 13, 2026 at 9:55 PM
You can find the PDF of the slides here: phil.ewels.co.uk/talks/2026/0...
Apologies for the dodgy audio on the recording! I tried fixing it but to no avail 🙈
Apologies for the dodgy audio on the recording! I tried fixing it but to no avail 🙈
The rewrite is not the nf-core pipeline, it's a separate project. The pipeline just calls a binary. The pipeline code is and always was MIT. The rewritten tool code I released as GPL-3, matching the strictest (and mostly consensus) license of the upstream software tools.
github.com/seqeralabs/R...
github.com/seqeralabs/R...
GitHub - seqeralabs/RustQC: Fast genomics quality control tools for sequencing data, written in Rust.
Fast genomics quality control tools for sequencing data, written in Rust. - seqeralabs/RustQC
github.com
April 13, 2026 at 12:45 PM
The rewrite is not the nf-core pipeline, it's a separate project. The pipeline just calls a binary. The pipeline code is and always was MIT. The rewritten tool code I released as GPL-3, matching the strictest (and mostly consensus) license of the upstream software tools.
github.com/seqeralabs/R...
github.com/seqeralabs/R...
For RustQC (in nf-core/rnaseq) we will use continuous integration snapshot tests to keep confidence that outputs remain identical (or functionally identical at least) to the outputs created by the original tools. Just 60x faster.
April 10, 2026 at 5:36 AM
For RustQC (in nf-core/rnaseq) we will use continuous integration snapshot tests to keep confidence that outputs remain identical (or functionally identical at least) to the outputs created by the original tools. Just 60x faster.