I've added an AI policy to ripgrep that was shamelessly copied from uv's policy. I plan to add this to the rest of my projects, but if anyone wants to offer feedback on wording, now would be a good time! github.com/BurntSushi/r...

lucumr.pocoo.org/2026/4/11/th... from Armin seems pretty related.

Deeply worried about deskilling in bioinformatics and software development. In parallel, also worried about low quality code being churned out rapidly by folks using these tools without doing proper quality control on the outputs 😬

We are often asked whether pangenomes are worth the hassle. The files can be large and methods to explore them are much more challenging than linear references. Earlier this week, we preprinted a clear example of how and why pan-genome graphs are so important for trait discovery.

still WIP but: better design-book examples incoming: meodai.github.io/design-book/

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

coming soon in a github.com/bearcove/figue near you

me: maybe i will finally write some of that code <gets immediately tarpitted for six hours trying to fix something in dev setup, is now 11:30>

I spent some time writing about a #rust library I've been working on: seqair, an alternative to (a subset of) htslib. This is a big one! So much potential API surface to cover and I better have a good reason for it! deterministic.space/seqair.html

This semester I developed and taught a course on applied population genomics. Lab activities proceed from the basics of the command line and Git to variant calling with workflow managers and a suite of downstream analyses (e.g., ADMIXTURE). All materials can be found here: elinck.org/genomics_eco...

From @davidmoreau.bsky.social & Kristina Wiebels in @plos.org #Computational #Biology | Nine quick tips for #software #containerization | I like all Tips, but particularly Tip 9: Plan for sharing & longevity | #Bioinformatics #Education #PLOSCBQT | 🧬 🖥️ 🧪 🔓 ⬇️ journals.plos.org/ploscompbiol...

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...

In about an hour using Claude Code (see disclaimer in repo) I put together code to do something that is a pain in the ass to do manually - find a good genome in NCBI then see what decent population level WGS data exist for that genome assembly in NCBI SRA: github.com/brantfairclo.... I'm impressed.

[blog] A Better R Programming Experience Thanks to Tree-sitter Did you know how Tree-sitter's support for R help you get ✨ reformatting through Air and linting through Jarl; ✨ auto-completion or help on hover in the Positron IDE; ✨ better search for R on GitHub; ✨ and more! By @maelle […]

Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes https://www.biorxiv.org/content/10.64898/2026.03.29.711974v1

The #snakemakehackathon2026 has ended, we are still preparing our preprint release. But, our host has prepared a note on their homepage: https://go.tum.de/946236 🥳 #snakemake #reproduciblecomputing

We've launched a department Trainee Emergency Fund, to help support EVERYONE BELONGING IN SCIENCE by meeting urgent financial needs of students and postdocs. Click to learn more about our goal with this fund and to donate! www.givecampus.com/schools/Univ...

🐍 For all ye #snakemake users out there who want consistent, opinionated formatting of their workflows: we have just released v1.0.0 of snakefmt 🥳 The major update is that it now sorts rule directives (e.g., input, output, resources, params, shell etc.). See github.com/snakemake/sn... for more

Another terminal based tool to interactively monitor all running #Snakemake workflows is #snkmt: github.com/cademirch/sn....

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'm hiring a postdoc in population and evolutionary genetics at Indiana University Bloomington! Computational lab. Message me if interested, and can apply here: indiana.peopleadmin.com/postings/32547

There's a "is anyone even reading this" sort of honesty you get in the software update release notes from a project that's been around for a long time.

Came across the phrase "cognitive DDOS" to describe our present culture. Understood instantly what it meant.

I’ve written a post about my recent experiences (successes) with AI coding models; the experiences that caused me to re-evaluate my initial judgements, the surprise I had at what can be accomplished, & some fears I have about these tools. Discussion welcome! combine-lab.github.io/blog/2026/02...

Excited for this. Teaching popgen is one of my favourite parts of my job and I've wondered about doing an online version of the class for sometime. Teaming up with @jrossibarra.bsky.social to do this is wonderful.

Playing with sandbox.bio. This was remarkably cathartic.

A succinct and useful list of rules for teaching data science, including some of my favourites: "teach with real data" and "have students do projects". #databs #datasky

I've just released #rust-htslib 1.0. After a long time with a pretty stable API usage of rust-htslib in production, it feels like the right time to finally move to 1.0. Most important change is probably a switch to thread-safe pointers in BAM record handling. github.com/rust-bio/rus...

Looking for something new to integrate into an #evolution or #microbiology course? Useful for lectures, labs, homework? Have a look at our STEPS program, which simulates bacterial evolution, including the #LTEE. Easy web-based interface & lab manual w/ exercises to help develop students' intuition.

vibe coding is the new doom scrolling?

Super-pangenome analyses across 35 accessions of 23 Avena species highlight their complex evolutionary history and extensive genomic diversity doi.org/10.1038/s415... Common oat=Avena sativa

Once more unto the breach: A fast introduction to snakemake, in 5 examples.

🚀 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

With population genetics on deck for #BI111 this week, preparations for HWE exercises for 1100+!students means lots of card-sorting!

I've slowly been reformatting notes from my population and conservation genetics course at Montana State University into a web book—a rough draft is now live here: elinck.org/popgen_conge...

🧬 Just out in Bioinformatics Advances: “tskit arg visualizer: Interactive plotting of ancestral recombination graphs.”  Read the full paper here: https://doi.org/10.1093/bioadv/vbaf302 Authors include: @kitchensjn.bsky.social, @yanwong.bsky.social

New special issue in Molecular Ecology on Conservation Genomics #popGen #evolution 🧪🧬🖥️ onlinelibrary.wiley.com/toc/1365294x...

Announcing bamdam: a new open source tool for studying ancient DNA 🧬 It shrinks massive metagenomic files by 10x and helps distinguish ancient sequences from contamination. Tested on the oldest DNA yet uncovered (2M years) link.springer.com/article/10.1... @bdesan.bsky.social @russcd.bsky.social

What a beautiful paper! www.nature.com/articles/s41...

@cademirch.bsky.social @erikenbody.bsky.social TB Sackton & @russcd.bsky.social introduce Callable Loci And More (clam), a tool that leverages callable loci to accurately estimate population genetic statistics (π, dxy, and FST). 🔗 doi.org/10.1093/molbev/msaf282 #evobio #molbio #compbio

The changed code is a small fraction of an open source contribution. Your commitment to understand the issue, how your proposed solution fits with the project, and be ready to own and push the review process forward is the biggest chunk of the work. Your effort is the contribution, not the code.

Friendly reminder that dishwashers made after 1995 or so are so water and energy efficient that even if you ran them twice fully loaded it would still use less water than handwashing the same load. So many "green" things feel like sacrifices. Dishwashers are not one of them.

Want to help shaping the future of #Snakemake? Then participate in the Snakemake hackathon 2026 in Munich! There's still room as the maximum number of participants is not yet reached. You can register here: indico.cern.ch/e/snakemake-... #sciworkflows #reproducibility

Check out the latest paper from the CCGP on California Quail and the ecological and anthropogenic factors that impact genomic variation. Led by Phred Benham and the Bowie group: onlinelibrary.wiley.com/doi/10.1111/...

Want to make publication-ready figures come straight from Python without having to do any manual editing? Are you fed up with axes labels being unreadable during your presentations? Follow this short tutorial including code examples! 👇🧵

Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.

Monthly Snakemake developer meeting: Tuesday, Sept 30th at 6am PST! Open to all - developers & users. We discuss issues/PRs and cowork on Snakemake projects. DM me to join! #snakemake #workflows #opensource #bioinformatics #oss

Preview of an important slide:

snkmt 0.2.0 is out! New features: 1. Multi-database support - switch between dbs via ctrl+p (like VSCode) 2. Workflow filtering - hide/filter by snakefile, status, or date for cleaner navigation github.com/cademirch/sn... #snakemake #bioinformatics #workflow #opensource #python #cli #tui