When they say “what’s the harm in one more day of antibiotics?”

Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it:

www.biorxiv.org/content/10.1...

Want to get started? github.com/rickbeeloo/b...

Pleased to see this pre-printed, highlighting the completeness/accuracy of @nanoporetech.com long-read genome assembly for clinical Enterobacterales: www.biorxiv.org/content/10.1...

Thanks to colleagues @modmedmicro.bsky.social, @ukhsa.bsky.social, @genewiz.bsky.social and @oxfordbrc.bsky.social!

🐎🦓 👀

🚨New post!

www.idstewardship.com/horses-zebra...

❤️ This looks like a really cool kickstarter to join if you are into medicine and games. Learning is hard, gaming can make it fun!

From the creator of @pharmageddon.bsky.social 🙌

cc @empiricgame.bsky.social #IDsky

ggplot2 hex with tada emoji. Text: Join the v4.0.0 release party with Teun van den Brand and the ggplot2 extenders, Oct 3 at 3pm Et, bit.ly/join-gg-extenders

The new ggplot2 4.0.0 is here! 🎉

This major update includes a foundational rewrite of S7 and user benefits such as smarter labeling and a revamped theming system.

Check the details: www.tidyverse.org/blog/2025/09...

BONUS: Join the release party on Oct 3, 3pm ET. bit.ly/join-gg-extenders

#RStats

Come see my poster at IMMEM Poster 151.

🔬 QualiBact – provides robust, data-driven QC thresholds for 304 bacterial species, built from >2.4M assemblies (AllTheBacteria + RefSeq).
⚙️ SpecCheck – an open-source command-line tool that applies these standards […]

[Original post on mstdn.science]

ESCMID strongly believes in the importance of unbiased scientific research and discussions amongst the global community. The ESCMID Executive Committee released a commentary on the recent political decisions made in the US.
www.clinicalmicrobiologyandinfection.com/article/S119...
#IDSky #Clinmicro

🏆 Research integrity consultant and image forensics expert @elisabethbik.bsky.social has uncovered fraudulent data in over 7,600 scientific papers and exposed the practices of ‘paper mills’ that produce counterfeit scientific articles. She is honoured with the €200K Individual Award. Congrats!

Are reads required? High-precision variant calling from bacterial genome assemblies Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared...

New preprint is out!
We investigate how well you can call variants directly from genome assemblies compared to traditional read-based variant calling.

Read it here: www.biorxiv.org/content/10.1...
Data & code: github.com/rrwick/Are-r...
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Why does @weare.rladies.org have less than 1000 followers? We can do better than this #rstats folks. It is a terrific account to follow because every week not only we get to know a new member of the #RLadies community but we also get to read their R favorites, tips, and jokes.

There's www.clinicaltrialsregister.eu but I'm not sure if it mirrors registrations in clinicaltrials.gov.

Since it's my week as curator 💜, let's dive into infectious disease modelling! 🦠📈

What do ID modellers do?
Use math, data & computer simulations to understand how diseases spread & how we can control them

It's a mix of
📊 Epidemiology
💻 Coding (eg #Rstats/ #Python)
🏥 Public Health

#IDSky #EpiSky

Bioart, courtesy of the NIH. All images are in the public domain and available for download as high-quality SVGs.
bioart.niaid.nih.gov

Introducing Rlinguo, a native mobile app that runs R - Rtask The R task Force - R experts for all your needs

#RStats

I'm so, so thrilled to finally share the release of Rlinguo, a mobile app that runs R 📱

This is a fully, native mobile app that uses #webR in the backend to run R functions.

Available on the App Store (iPhone) & Play Store (Android)

rtask.thinkr.fr/introducing-...

Picture of a plaque assay (purple field with clear holes) showing gorgeous poliovirus plaques

My replies are perpetually full of anti-vaxxers these days telling me about polio vaccines.

Not shockingly, most of what they are saying is wrong. Luckily, I trained with Vincent Racaniello & he taught me a few things about poliovirus.

So let’s discuss the king of the Picornaviridae👇🏻

Guideline says to take 3 sets (6 bottles total) from at least two punctures if suspected intravascular infection. I suspect we're rarely asked, but that's the advice we give when asked

One puncture, 4 bottles. Pretty standard in Denmark, reasonably low rates of contamination. clinicians trained to ignore Gram positive cocci in clusters 1/4 bottles by comment on the sample and the fact that it doesn't trigger a call from the lab as opposed to other findings

Hi folks. My name is Adi Shah, ID doctor at the Mayo Clinic. I love medicine and helping people. I used to make jokes on twitter and don’t take myself too seriously. I am also an immigrant 🇮🇳 🇺🇸 Hello 👋 😀

a white door with a hole in it that looks like a hole in a wall ALT: a white door with a hole in it that looks like a hole in a wall

Are there an medical microbiology or infectious diseases starter packs out there?

Microflora Danica: the atlas of Danish environmental microbiomes bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Thank you very much team Aalborg for having invited us to become part of this journey to map the environmental microbiome of an entire country. Super exciting findings and a whole section on #nitrifier diversity and abundance in Denmark #MicroSky 🧪

www.biorxiv.org/content/10.1...