Antoine Limasset

Multi-context seeds enable fast and high-accuracy read mapping - Genome Biology A key step in sequence similarity search is to identify shared seeds between a query and a reference sequence. A well-known tradeoff is that longer seeds offer fast searches but reduce sensitivity in ...

1/ Our paper on Multi-Context Seeds is now out, with @tolyan.bsky.social spearheading the work and contributions from Nicolas and @marcelm.net. We introduce a new seeding concept that improves read alignment accuracy while maintaining speed.
link.springer.com/article/10.1...

I think their plan is that they still have orders of magnitude inference improvement in sight so they will be able to keep this kind of subscription in the future while the adoption war is happening right now and they know this is usually a winner takes all

RNA-seq analysis in seconds using GPUs https://www.biorxiv.org/content/10.64898/2026.03.04.709526v1

kallisto sped up RNA-seq quantification by 50x. Now another 50x speedup... quantify hundreds of millions of reads in a few seconds.

This seems too good to be true. But it's true!
Incredible accomplishment by @pmelsted.bsky.social.

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

COMBINE lab COMputational BIology and Network Evolution lab. COMBINE lab has 137 repositories available. Follow their code on GitHub.

Dear @anthropic.com, my lab builds a lot of OSS for genomics (github.com/COMBINE-lab). While we lack the widespread OSS market of popular NPM packages, pieces of our software are critical in biomedical research. Please consider extending your Claude Max offer to such labs!

Very interesting issue!

Contemplating migrating repos to Codeberg again, again facing the issue of CI infra. Is there any solution that offers even a fraction of what GitHub gives public repos *for free*? I can't afford this much cloud credit, nor a server (thanks Nvidia).

I may play around a bit more tonight, but this is a good checkpoint: github.com/COMBINE-lab/.... All features implemented, unit and integration tests, dedicated aarch64 & avx2 backends, a driver CLI! Still a bit slower than the C version, but we're closing the gap quick!

I still think that you hit a wall at some point because of the codebase size because of the limited context size(always the same issue)

Trying an experiment. I want to use WFA2-lib in Rust. But, I don't want bindings (I am so *over* having C or C++ deps in by build chain). So, I'm going to make a Rust native port with Claude Code. I started at 2:03PM. I'll provide an update (or an implementation) by the end of the day :).

Great to see this work out, led by Jon Rosen and co-supervised Karen Mohlke @klmohlke.bsky.social!

Connecting to some recent threads here:

This is so f**** up

After years of work, the centerpiece of my PhD is published in @natmethods.nature.com! Read it to learn about the biophysical insights we can get from single-cell data!

But first, I would like to talk a bit about RNA velocity and normalization. 1/

Monod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing data - Nature Methods Monod fits biophysically motivated models to single-cell transcriptomics data, empowering multifaceted and integrative insights of gene expression dynamics, stochasticity and regulation.

Monod fits biophysically motivated models to single-cell transcriptomics data, providing insights into gene expression dynamics. @goringennady.bsky.social @lpachter.bsky.social

www.nature.com/articles/s41...

Dear @anthropic.com please consider extending your Claude Max subscriptions to open science software devs! Our repos may not have as many stars as those of some of our OSS peers, but we develop critical infrastructure in focused areas, and might even benefit more from what Claude Max offers!

MetaStrainer: Accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples. https://www.biorxiv.org/content/10.64898/2026.03.02.709061v1

When someone says „Scientists do not want you to know“ you can dismiss everything from there on. Scientists want you to know. They are desperate that you know. They can’t shut up about what they found out and want you to know.

Hey ChatGPT, write me a fictional paper: these LLMs are willing to commit academic fraud Mainstream chatbots presented varying levels of resistance to deliberate requests for fabrication, study finds.

The findings “should act as a wake-up call to developers on how easy it is to use LLMs to produce misleading and low-quality scientific research”

go.nature.com/4u4SBBP

I am always amazed by webassembly applications!
Curious about how hard it is to get this from existing Rust code

GitHub - COMBINE-lab/ksw2rs: a native rust port of the KSW2 alignment procedure a native rust port of the KSW2 alignment procedure - COMBINE-lab/ksw2rs

Point of comparison, Codex 5.3 did a nice initial conversion of ksw2 (just extz) to Rust, with reasonable eprf. It was unable to close the perf gap with C. It couldn't identify the key bottleneck. Claude Code (sonnet 4.6 even!), came in, thought for a bit, and nailed it. github.com/COMBINE-lab/...

Introducing kuva: A scientific plotting library in rust, along with cli binary with the option to plot directly into the terminal.

Feel free to drop me some feedback as an issue on the repo

github.com/Psy-Fer/kuva

crates.io/crates/kuva/...

Speedrunning Rust translation before the Butlerian Jihad?

The US is broadly a country that likes to invest in science. Even among Republicans this is true. But we are governed by an administration that is opposed to science, and is using procedural tools to limit spending and increase political control over the process.

The first fully Rust version of piscem! scRNA, scATAC, and bulk-RNA -> RAD files, accurately, in low memory, and FAST. And all in Rust :) anaconda.org/channels/bio...

Most programmers are taught that L1 is the “top level” cache on x86.


It’s not quite true anymore!


Intel calls it the Decoded Stream Buffer (DSB), AMD the OpCache.

Only enough room for ~4,000 micro-ops, but there are interesting ways to take advantage of it.

Release SeqKit v2.13.0 (10-year-old birthday version) · shenwei356/seqkit Changelog SeqKit is 10 years old! SeqKit v2.13.0 - 2026-02-28 seqkit: add support for reading and writing LZ4 compression format. new command: seqkit sample2: improved seqkit sample by @stahiga....

Can't wait to release a 10-year-old birthday version for SeqKit!

- 10 years
- 2 papers, 3500 citations
- 20 contributors
- 40 subcommands
- 880 commits
- 500 issues
- 685.5K Bioconda total downloads

Thank you all, dear contributors and users!
I'll keep maintaining it.

github.com/shenwei356/s...

Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025.
allthebacteria.readthedocs.io/en/latest/ov...

“The purpose behind the release of herbicide on the villages remains unclear.”

Israel has been dumping herbicides throughout southern Lebanon as part of a concerted ecocide campaign to render the region uninhabitable. This has been going on for months with Lebanese journalists & environmentalists regularly reporting on it.

The BBC: we don’t know why the Israelis are doing it

‘Don’t go to the US – not with Trump in charge’: the UK tourist with a valid visa detained by ICE for six weeks Karen Newton was in America on the trip of a lifetime when she was shackled, transported and held for weeks on end. With tourism to the US under increasing strain, she says, ‘If it can happen to me, i...

A retired British primary school administrator with a British passport and a valid visa was shackled, chained and detained for six weeks by ICE

www.theguardian.com/us-news/2026...