I really think the net benefit for society is greater if we banned social media for those over 16.

💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...

Big news!

🧬 Come check out my poster on agtools, an open-source Python framework for analysing and manipulating assembly graphs at #ABACBS2025 Poster #106 • 💻 Github: github.com/Vini2/agtools 📄 Preprint: biorxiv.org/content/10.110…

End qualified immunity.

PubMed is running on autopilot during shutdown, but key independent committee has been abolished www.bmj.com/content/391/... 🧪

Graduate seminar did a deep dive on Thomas Paine’s Common Sense yesterday. At the line, “in America the law is king,” they (14 students from 6 countries) burst out laughing. I've been doing this for 35 years and this is the first time that was a laugh line.

You know you work for a software company when the description of meeting room names in your new office comes with regex that they will all follow.

Our new preprint is up! This is the main postdoc work of @wiesner-t.bsky.social focusing on exocytosis along the axon shaft and its regulation by the sub membrane actin-spectrin scaffold: www.biorxiv.org/content/10.1... Read the thread below for a summary of our findings 🧵1/11

New blog post – A quick look at Roche's SBX lh3.github.io/2025/09/11/a...

Now published in GigaScience with minor improvements: academic.oup.com/gigascience/... * Download: zenodo.org/records/1490... * More info: github.com/lh3/panmask

Plants phylogeny is a mess anyway Credit : @xkcd.com

Always relevant.

My 6th grader is doing a survey for ethics class on the concepts of happiness and luck (or Glück for the German speakers). If you have a few minutes to submit your thoughts she’d appreciate it. docs.google.com/forms/d/1y2b...

These are VERY rough estimates, but here's life expectancy after diagnosis of type-I diabetes over the past 150 years. It was Banting and Best's discovery of how to isolate insulin in 1921 — not some fucking cooking class — that gave people including my daughter a new lease on life.

I’m overwhelmed by the expressions of sympathy and support. And still this pales in comparison to what they are doing to immigrants and to undermine the Bill of Rights. If you could do one thing for me, call your representatives and demand accountability for their white supremacist terrorism.

This seems like a good thing. Are we aloud to have good things? I feel like this is going to turn into a Charlie Brown and Lucy with the football sort of situation.

Anyone want to go in on an industry collab to fund this?

I've seen enough. Donald Trump is not abiding by a lawful Supreme Court ruling. As a member of Congress, I fully support impeaching him. NOW.

How is this Python package real pypi.org/project/tari...

Cruel Fate, 1525: Our cow died during the night. We will surely perish. Cruel Fate, 2025: Our Keurig stopped working during the night. We will surely perish.

That’s a wild backdoor…

Burn

Someone needs to do a dramatic reenactment of this

Is this the legal equivalent of questioning a 4 year old that is denying having eaten chocolate while they have chocolate smeared all over their face?

#standupforscience #clermont-ferrand

Great, let’s loosen controls on snake oil, just what we need more of.

There are trans Americans right now looking out at this world and wondering if anyone is going to stand up for them and for their simple right to exist. Well, I am. We are. We will.

How many others had Latin back in the day and read this as SPQR chemistry at first?

Excited to work with Rob's team on extending the salmon/tximeta/Bioc tool chain for long read quantification with oarfish. Lots of interesting challenges but plan to deliver the same high level of provenance detection automatically 🤖

This is very cool work and I'm happy to see it published. Vcfexpress by @brent-p.bsky.social and @aaronquinlan.bsky.social allows building (essentially) arbitrary VCF filters expressed in lua code with parsing & eval powered by rust! academic.oup.com/bioinformati...

Someone has apparently been fucking with the NIH’s nameservers

/3 Let me repeat that: “I don’t want to talk to you. I want to talk to a lawyer.” In all other respects, shut the fuck up. Don’t engage them. Don’t let them engage you. They are not trying to help you. They are not trying to “clear this up.” Shut. Your. Fucking. Mouth.

Finally; the preprint on Cuttlefish 3 is available! This is the most recent in a long line of work led by Jamshed Khan, a recent PhD graduate from my lab. Cuttlefish 3 further improves the efficiency of Cuttlefish 2, while adding support for *colored* compacted de Bruijn graphs. 1/x

🚨 BREAKING: OMB has just issued a memo *rescinding* the previous memo freezing all federal financial assistance programs. Full text, per government source:

The final publication related to my post-doc time has finally been accepted for publication…almost 10 years after leaving that lab and 5 years after moving to industry. Much respect to those still slogging it out in academia, may your patience and hard work pay off :)

Congratulations to Claudia Keller Valsecchi for receiving the prestigious Friedrich Miescher Award. This prize is Switzerland's highest distinction for young scientists working in the field of biochemistry. www.biozentrum.unibas.ch/news/detail/...

I think we have a problem with survivorship bias. Lots of people felt like, "well, they said it would be terrible in the first Trump term, but I'm still here, so it was fine and they lied!" And so not only is Trump re-elected, people aren't even resisting in any sense this time around.

💯 Your time is usually worth more than the cost of redoing that crappy batch of RNAseq.

By popular demand, bioRxiv Bsky posts have been switched to a condensed format . The inability to control sizing of images on Bsky meant these were large and clogging people's timelines. We listened 😀

Instead of chastising people for speaking ill of the dead, I’d simply encourage people to live in such a way that there would be no debate about whether their death was a net benefit to humanity.

Writing shell wrappers is hard, part #649: singularity exec image bcftools stats -i 'DP>10 && QUAL>10' … Hard to be sure from this report, but it appears that `singularity exec image` is not propagating the quoting correctly. github.com/samtools/bcf...

CHARLIE BROWN: happy thanksgiving! CHARLIE BROWN’S PARENTS: wah wah wah CHARLIE BROWN: I cannot believe you said that that’s racist CHARLIE BROWN’S PARENTS: wah wah wah CHARLIE BROWN: he’s not my President CHARLIE BROWN’S PARENTS: wah wah wah CHARLIE BROWN: I am too your son

If anyone else on here will be at the IABS meeting on NGS in Frankfurt next week then say “hi” while there. It’s always nice to put a face to the online handle.

Just out: @multiqc.info v1.25.2 🎉 This patch release fixes a whole host of bugs, the most important one being for #bcl2fastq 🐛 There are also a host of small additions sneaking in for #ngsbits, #picard, #Nanostat, #Samtools and more - so well worth the update! github.com/MultiQC/Mult...

I have made a new release of kyber, a tool to make a quick sketch of your long-read sequencing data or to compare multiple datasets. It uses a fixed grid of accuracy and read length. Now also supports ubam - feedback appreciated! github.com/wdecoster/ky...

Just out - our paper on a successful phase I trial of DNA vaccines against triple-negative breast cancer! genomemedicine.biomedcentral.com/articles/10.... Key points: - Neoantigen specific T cell responses were induced in 14/18 patients - 87.5% recurrence-free survival at 36 months Thread below!

This is a very important idea, and worthwhile for those developing bioinformatics software to consider. One massive shortcoming, over which the scientists & devs have quite little control, however, is the huge dearth in funding software dev & maintenance. Software is its own product & requires $!