I don't understand rewrites.bio at all. Most bioinformatics software is distributed with a license. The license specifies exactly what is and is not permitted to do with the software. Yet now one is supposed to ignore the license and adhere to requirements specified by someone on a website??

www.pnas.org/doi/10.1073/... If you ever need lto be convinced by how bad the "Contributed by" track is at @pnas.org ... Only author: David Lipman, handling editor: David Lipman. Only integrity-free person not embarrassed by such a paper: David Lipman. Even uses "I did" in the abstract. Shameful.

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...

If you work in genomics and haven't thought about vibe coding yet — episode 150 is your wake-up call. #microbinfie #genomicx

🤯 y'all... I have been on the edge of my seat waiting to show you this episode. Not only is it the 150th episode of #microbinfie but we show you some pretty outrageous vibe coding. 🫨 Let us know what you think with #microbinfie #genomicx pca.st/episode/3784...

We just uploaded the 150th episode of the #microbinfie podcast, scheduled for Thursday, where we blow your mind with vibe coding. I can't believe we have actually made it this far. 🍻 To the next 150 episodes 🥂 @happykhan.mstdn.science.ap.brid.gy @andrewjpage.bsky.social

Huge blind spot on #riskyornot! @benchapmanncsu.bsky.social @bugcounter.bsky.social

Joining the All-The-Bacteria project provides an annualised return on investment of 8.9% bacterial genomes.

Running CDC is not a part time job or an afterthought and the agency needs stable leadership @medpagetoday.com @gfriedman.bsky.social @altcdc.altgov.info

BRIG v1.0.0 Released — BLAST Ring Image Generator This is dedicated to Joe Healey Who asked me many years ago to round up the version number to v1. BRIG creates circular comparison images showing sequence similarity between a reference genome and multiple query sequences as concentric rings — […]

🪧New patch for Kalamari, a database of reference genome assemblies, backed by subject matter experts! 🧫New bacterial respiratory pathogens 🥔Precompiled Mash database conda install kalamari 🦑 github.com/lskatz/Kalam...

I used it to create a microbial bioinformatics G-Funk 90's rap snippet 😆 gemini.google.com/share/1df0e1...

Day 1 in a new lab: “You’ll be working on this organism now.” Me: cool cool cool (has never heard of it) I wrote the checklist I use to survive that situation: 👉 self-onboarding a new pathogen lskatz.github.io/posts/2026/0...

Just added a measles genome (subtype D8) to Kalamari. Useful for screening + as a reference genome - and a reminder that we still maintain a living list of public health reference genomes. Measles is relevant again. Infrastructure matters. 🦑

More than a week after his death, I’m still reflecting on the life and legacy of Bill Foege—the Babe Ruth of public health—whose work with others saved the lives of literally hundreds of millions of people. His accomplishments are in a league of their own.

Happy Groundhog Day to all those who enjoy orderly shutdowns

@planetmoney.bsky.social have you seen Wonder Man yet?

(1/2) MMWR: Measles Outbreak Linked to Air Travel — Colorado, 2025 An unvaccinated traveler exposed others during an international flight and at Denver International Airport, leading to: • 9 secondary & 1 tertiary case in Colorado • 7 more cases in other states • 4 hospitalizations, mostly unvaxxed

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...

After being held in two of them as a boy, I fought for decades urging America to never again build concentration camps and put human beings in them. It breaks my heart to watch this happen twice now in my own lifetime.

@openargs.bsky.social goddam you guys are great. Keep it up 👏 pca.st/episode/56ba...

> An alternative to GISAID has been gaining ground. In 2024, Chen, Stadler, and others launched Pathoplexus, a platform that also seeks to protect the interests of those uploading sequences but aims to allow data to be shared more freely. And if you love podcasts: open.spotify.com/episode/0wrp...

Just a couple shots protect you from having to bury your child. THIS ISN’T HARD. VACCINATE!

Happy anniversary of Jesus's bris to those who celebrate

Happy new years for those who celebrate

Literal LOL from me when the Jewish chief comes into the church breaking out her Yiddish

I just completed "Secret Entrance" - Day 1 - Advent of Code 2025 #AdventOfCode adventofcode.com/2025/day/1 I did it in scratch! scratch.mit.edu/projects/126...

Revisiting this classic today en.wikipedia.org/wiki/Deaths-...

'Denmark explicitly declined to add rotavirus vaccination. Their health authority concluded that rotavirus infection “hardly ever results in death or long-term harm” in a country with universal health care access.'

The media needs to stop writing headlines like “The CDC changes course on vaccines and autism” and “The CDC defends measles response”. NONE of this is coming from legitimate scientists at the CDC. ALL of it is coming from RFK Jr. Every such headline is causing further harm to public health.

Honestly, as a micro binfie, I couldn't feel more honored than to be entrusted with this! 😃 Prokka has served so many so well, and deeply inspired me how to write Bakta. I'm thankful to be part of this open science com, and will do my best to meet these high quality standards. Thanks Torsten! 🦠💻

💾 Shovill 1.4.1 has been released! The best way to de novo assemble microbial genomes from Illumina FASTQ. Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking. #bioinformatiocs #genomics #microbiology github.com/tseemann/sho...

I just looked up my notes from 2014 when we were in the rhythm of it all, uploading thousands of genomes. It was like five one liners in perl, some curl commands, and a combination of bash and python scripts. Documented in NOTES.txt. Bioinformatics was wild.

WCHA disagrees with CDC’s Advisory Committee’s change to decades-long vaccine recommendation that has reduced pediatric hepatitis B infections by 99 percent. doh.wa.gov/newsroom/wes...

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

I can't help but notice that #pizzintwatch doesn't track pizza places close to CDC.

Did you hear about the fight between the fork and the turkey? It was tine-y and short lived. Happy Thanksgiving!

Weaponization of the premier public health agency in the country for personal clout and gain. The CDC website should not be trusted given the fact that it is controlled by people who will profit from spurious and false attempts to link vaccines to autism. www.cdc.gov/vaccine-safe...

I'm predicting it now for #pluribus on #appletv now: an ancient civilization from Earth 1.2B years ago got this virus but wanted to propagate it into the future.

The last episode of the three part debate is out today! Check it out on the platform of your choice 🤩 Don't forget to give us stars and reviews to help spread the podcast to new listeners!

On #foodsafetytalk, the podcast co-hosts said that the food safety world needs something like a federated and possibly industry-led system for regulators. I wonder if this extends to genomic epidemiology? Let me take you on a tangent.

We hope you'll join us tomorrow night at 7 for our first episode!

We are a two fed family, so no income for 40 days. I am incandescent with rage about the Dems caving.

pre-writing a devastating obituary for your enemy is god-tier hating of a kind you don’t often see anymore. renaissance haterism. beautiful stuff.

That would have been big news a few years ago, unfortunately the great science that gives important understanding in coronaviruses is now back to the small circle of scientists. Anyway: A fully functional furin cleavage site in a bat betacorarnavirus! Congrats to the authors!

My former mentor, colleague, and friend Hamilton Smith passed away this week. He was a giant in science, a Nobel Laureate, but also one of the nicest people you could ever meet. He will be missed by many. www.jcvi.org/media-center...

Proud of the latest edition of my free intro biostats book. gitrepo: github.com/ybrandvain/b... book: ybrandvain.github.io/biostats/ Not complete but at a good point to take a break, and I think its quite usable dm me with comments , ideas etc

Just another normal HHS week: CDC researchers cannot present work at an annual Infectious Disease conference in (checks notes) Atlanta. As a CDC researcher put it: “It appears to me that HHS’s goal is to prevent the dissemination of scientific information. It’s insane.” apnews.com/article/infe...

🚀 New in Fasten: fasten_head Unix head, but FASTQ-aware 🧬 ✅ Get first N reads (not just lines!) ✅ Works with paired-end reads ✅ Can limit by bases OR reads ✅ Blazingly fast (it's Rust 🦀) cat huge.fq | fasten_head -r 1000 Stop doing math with -n. Let the tool understand your data.