Robert Aboukhalil

Winner winner arxiv.org/pdf/2610.27918 "AI disclosure. During the writing of this paper, we had several conversations with Claude, 55, owner of the neighborhood bar in Strasbourg. Unfortunately, none of them was of relevance to the topics of the paper."

Always love seeing more educational content on a topic that helped launch my academic career!

Thanks to everyone who signed up for our data analysis study! There's still time to sign up, as the survey goes out tomorrow (Oct 21). If you work with data in your research, it will only take 3 minutes and it's anonymous: sandbox.bio/study/data-a...

New blog: Emu runs an order of magnitude faster for high quality (sup) R10 @nanoporetech.com 16S data, with the lr:hq preset for minimap2, in addition to improving downstream analysis as previously blogged by @mbhall88.bsky.social: livingsystems.cc/posts/lrhq-s... #bioinformatics #microbinfie

AI CEOs keep predicting the end of disease, while pharma CEOs have a much more thoughtful take on how AI is actually speeding up the drug development timeline: youtu.be/ukZvIjq2oJc

I made a Nextflow tutorial you can run from your browser!! Nothing to install, and cloud costs are sponsored by @carolinacloud.io You build a pipeline to find how much sequencing you need to detect Listeria in ice cream, with interactive challenges along the way. sandbox.bio/tutorials/ne...

I can't believe it's already been 5 years since I first released sandbox.bio! 🥳 To celebrate, next week we'll release one new feature every day of the week. Follow along at sandbox.bio/anniversary, or here on BlueSky.

Great write-up on the work my colleague Xinglin has been doing.

Explore the HPRC Year 2 pangenome graph with Graphoscope. Search a gene or genomic region to visualize the pangenome graph at that locus with no pangenome data or specialized setup required. Try it here: marianattestad.github.io/graphoscope/...

grep is a fantastic tool, but it doesn't really work on sequencing data: it breaks when the pattern is in the read name, and doesn't support paired-end FASTQs. Thanks to @nilshomer.com, we have a new interactive guide on using fqgrep to find patterns in FASTQ files: ➡️ sandbox.bio/tutorials/fq...

DIAMOND v2.2.4 is available today, providing compositional matrix adjust for the clustering workflows and more. github.com/bbuchfink/di...

Ever wanted to quickly check host content of DNA sequences? bede.im/sapiometer

Prompts are available from the corresponding author upon reasonable request.

Senior Bioinformatics Software Developer opening in my team in ONT's Applications department! Hybrid with a few days a week in our Oxford headquarters. We can sponsor visas! www.linkedin.com/jobs/view/44...

Check out our new Makefile tutorial if you want to finally understand what those "make install" commands actually do when you paste them in your terminal, and how to use them in your work: sandbox.bio/tutorials/ma... Thanks to Stephen J Bush for contributing this tutorial!

How good is MiniBWA, the successor to BWA? To test it, I ran MiniBWA on sequencing from 76 different species, comparing mapping speed, rate and accuracy with BWA MEM. In short, it's really good. If you map short reads, it's well worth your time. andrewcarroll.github.io/2026/06/30/t...

New on sandbox.bio: a FastQC playground you can use for teaching QC analysis of sequencing data. It runs entirely in the browser, GUI and all (thanks to CheerpJ and WebAssembly!) ➡️ sandbox.bio/playgrounds/...

Okay I'm sorry if you're all getting tired of it, but here's yet another I-built-this-with-AI post. It is my first time really vibe-coding something, but it's for a good cause: updating my old academic software Assemblytics that I had nearly shut down multiple times due to server issues.

salmon 2.0 (the rust re-write) is now live! It's also the version you get if you install via bioconda. This is a from-scratch rewrite in rust, and the base for future development. I'll post a more detailed thread tomorrow, but you can read the docs here combine-lab.github.io/salmon/

scverse conference 2026 will take place in Copenhagen, October 12–14. ✨ Three days of all-things-single-cell and open-source tooling and community in real life. More details soon but for now, mark your calendars. scverse.org/conference20... See you in Copenhagen 🇩🇰

This seems like an awesome opportunity for people looking to pick up Rust experience and contribute to a very cool project! I hope for typst to become the standard for writing structured scientific and mathematical documents, saving us from the tyranny of LaTeX and the insanity of Word!

It was great fun talking to @robert.bio and his edit is great (I love some of the overlays, especially the one about @robp.bsky.social being an authority 😂)

I've seen lots of AI rewrites in bioinformatics lately, and I’m concerned because LLMs can be confidently wrong. What do the best tool builders do to make sure their rewrites are correct? How can we tell if a rewrite is flawed? I interviewed 5 scientists to find out: youtu.be/0o2XnEBDxrI

Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.

From @robert.bio @helenechiapello.bsky.social @mthomaschollier.bsky.social & col. in @plos.org #Computational #Biology | Training biologists in #Unix command-line skills: From curriculum to interactive online tutorials|#Education #OpenEducationalResources | 🖥️ 🧪 ⬇️ journals.plos.org/ploscompbiol...

Host read removal sounds simple. It's not. 🧫 Ep. 151 of #microbinfie: we talk with @bede.im about Deacon — why alignment-based approaches fall short, the sensitivity/specificity tradeoff, and what it takes to remove host reads at scale. Part 1 of 2. #metagenomics on.soundcloud.com/gEm7QyaTauvd...

Just finished teaching another semester of Genomic Data Visualization! 🥳 This semester, I integrated AI-assisted vibe coding. Some students used AI to excel beyond the mechanics of coding. Others struggled in ways I did not expect. I reflect on my blog: jean.fan/2026/03/15/v...

Wow, this is amazing @wytamma.bsky.social!

I saw a Youtube video by @omgenomics.com profiling the work that @plasmidsaurus.bsky.social has been doing in streamlining sample preparation for their Plasmid sequencing and RNA-seq products. Interesting to see @OpenTrons instruments *everywhere*, and how they turn operations "pipette triggers".

We just released a video from our visit to @plasmidsaurus.bsky.social, where we spoke with Mark Budde and team: www.youtube.com/watch?v=nS2o... Highlights include: ✅ 3D printed magnetic bead contraptions ✅ When sequencing more is easier than sequencing less ✅ Bread machine analogies

Playing with sandbox.bio. This was remarkably cathartic.

That tech oligarchs are noisy and incensed about the remote possibility of a wealth tax and utterly silent about the murder of a man who was only using the phone they invented to chronicle the thuggish government goon squads should tell you everything about these desiccated souls.

🚀 Our new paper on Alignoth just published in Bioinformatics! Alignoth generates self-contained interactive HTML read alignment plots from BAM files – Rust-based, portable, and ideal for headless workflows. 📄 doi.org/10.1093/bioi... #bioinformatics #genomics #rust @johanneskoester.bsky.social

Blogpost: I took an oral probiotic for a month and did microbiome sequencing at @Plasmidsaurus. blog.booleanbiotech.com/oral-microbi...

Releasing alignism, a small tool that I have found useful for doing multiple sequence alignment in browser. hgbrian.github.io/alignism/ - The hard work was done by the awesome biowasm team! - Does tree building too - V fast compared to e.g., muscle on EBI - Not tested that much!

I've been thinking about the "virtual cell" concept and wanted to write up a few thoughts. Specifically on how I think the prior experience in GWAS informs the most likely way these models will be useful. andrewcarroll.github.io/2025/12/23/t...

One last bioinformatics puzzle before the holidays: Can you figure out the file formats of unlabeled sequence data? 🎅 sandbox.bio/puzzles/form...

These are fun educational puzzles to improve debugging skills of students! thanks to @robert.bio for creating these sandbox.bio/puzzles

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n