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

Keith Robison@omicsomics.bsky.social · 3d ago

When PCR Gives You Lemons... A Danish group has peered into PCR artifacts and turned them into a fascinating way to index genome libraries omicsomics.blogspot.com/2026/08/when...

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...

Interactive bioinformatics tutorials

Learn bioinformatics from your browser, no setup required. Everything runs in a sandbox, so you can experiment all you want.

sandbox.bio

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

GitHub - bbuchfink/diamond: Accelerated BLAST compatible local sequence aligner.

Accelerated BLAST compatible local sequence aligner. - bbuchfink/diamond

github.com

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!

Intro to Makefiles

Interactive make tutorial: learn to use and create your own Makefile using a command-line interface in your browser.

sandbox.bio

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 🇩🇰

scverse conference 2026

scverse.org

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!

Typst@typst.app · 2mo ago

Get paid to work on Typst by joining our new limited project PDF Forms. It's a great opportunity to get professional experience for Rust through open source contributions this summer. More information on how to apply at typst.app/jobs/.

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 😂)

Robert Aboukhalil@robert.bio · 3mo ago

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

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

I interviewed 5 bioinformatics experts about AI rewrites

YouTube video by OMGenomics

youtu.be

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...

Training biologists in Unix command-line skills: From curriculum to interactive online tutorials

As the generation of data in the life and health sciences expands rapidly, there is a growing need for professionals and students in these fields to master core bioinformatics skills, particularly tho...

journals.plos.org

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...

151 - Deacon part 1

In this Software Deep Dive episode, we talk with Dr. Bede Constantinides (University of Birmingham) about Deacon, a tool for removing host DNA reads from metagenomic datasets. We discuss why host read

soundcloud.com

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!

Wytamma@wytamma.bsky.social · 5mo ago

At the #SnakemakeHackathon2026 in Munich last week I complied Snakemake to #Wasm and made a client-side webapp for creating and sharing workflows -> snakemake.github.io/snakemake-wa.... It has support for python, R, and a 32bit linux environment all running in your browser ❤️ 🐍

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

The "Why Not?" Era of Sequencing Has Begun

YouTube video by OMGenomics

youtube.com

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...