Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

This tool looks incredible, I've been missing something exactly like this to analyze assembly graphs, which is necessary to understand more complex genome structures.

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

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N

Definitely hard to measure, but here is our best attempt from a new benchmarking paper to be preprinted in the next few weeks. Element appears to be the current king of homopolymers. Illumina does worse than HiFi beyond 20 bp. (This is all measured on human DNA)

New blog post! I added a new feature to @gbouras13.bsky.social's Pypolca: homopolymer-only polishing. Potentially useful for cross-sample polishing - early test on Cryptosporidium looks promising. Check it out here: rrwick.github.io/2025/09/04/h...

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

Maybe I am being grumpy, but can people please stop using poorly curated databases of antibiotic resistance genes (I am looking at you, DeepARG) on shotgun metagenomic data and then present these results without any reflection on their validity, or shortcomings of databases?

The TaxTriage paper www.biorxiv.org/content/10.1... has a discussion of this that I still need to grok. It's kind of mentioned as an aside in the main text, need to dig!

Streptomyces venezuelae uses secreted chitinases and a designated ABC transporter to support the competitive saprophytic catabolism of chitin vs Bacillus subtilis @plosbiology.org by Anne van der Meij et al from Justin Nodwell with Marie Elliot journals.plos.org/plosbiology/...

Just out: metagenomics with internal standards yields phylogenetically resolved genome ("~cell") counts of bacteria, archaea, and photosynthetic eukaryotes per L of seawater, over the AMT29 Atlantic transect, via "single copy" genes (recA, radA, psbO). Compares with microscopy and flow cytometry.

Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. arxiv.org/abs/2506.12986

A female Western Gull was recorded riding 150km in a garbage truck from San Francisco to a compost facility in Central CA, probably to forage. TWICE. An innovator, an icon, a genius. This is one of my favorite @waterbirdsociety.bsky.social papers I've ever handled as managing editor #ornithology

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

ARTIC 2 is here!

@lh3lh3.bsky.social's latest assembler has really pushed using "routine" ONT libraries (N50s 30KB ish) to get to near T2T assemblies, leveraging read length for (diploid) error correction. Heng continues to be the fountain of excellent sequence bioinformatics tools and it impressive to see.

An antisense RNA regulates production of DnaA and affects sporulation in Bacillus subtilis PLoSGenetics from Alan Grossman journals.plos.org/plosgenetics...

🚨 Teaching bioinformatics? Or learning it solo? Check out my free & open Fundamentals of Bioinformatics course materials: lectures, slides, and exercises — no coding background required. 🔬🧬👩‍💻 📚 github.com/lskatz/funda... ⭐️ Star it, share it, and level up! #bioinformatics #opensource #STEMeducation

Unpacking policy developments in marine natural product research: a scientist's guide to DSI and BBNJ @natprodreports.rsc.org pubs.rsc.org/en/content/a...

www.biorxiv.org/content/10.1... Searching for lytic phages in bacterial genome assemblies ..!

Europe will always stand for science and the freedom to learn and invent. As of 11 am, tune in, and discover how the @ec.europa.eu wants to help the best and brightest ‘Choose Europe’. → europa.eu/!Tx43kH

"That telomere phages are so prevalent means that they are a selective force, one that we know little about. We now want to understand how the telomere-toxin is secreted and also understand how this ‘telocin’ wheedles its way into unsuspecting bacterial neighbors” www.science.org/doi/10.1126/...

Excited to share new research led by our very own @lingdong-shi.bsky.social showing that many archaeal 23S rRNAs are circularized in active ribosomes. Check out the preprint below.

Genomes from long-read metagenomic assemblies contain rampant errors, highlighting the pressing need for stricter evaluation methods in long-read assembly algorithms. Read more in our paper with the Eren group. @floriantrigodet.bsky.social @merenbey.bsky.social

We're happy to announce that the #antiSMASH v8 paper is out in @narjournal.bsky.social: academic.oup.com/nar/advance-... Many thanks to @kblin.bsky.social, @marnixmedema.bsky.social and many international collaborators!

"Ecologist Katharyn Boyer must shutter the beloved marine research center she manages on the San Francisco Bay’s shores — unless she can raise millions of dollars by next week. Scientists, conservationists and community members statewide have rallied to save the Estuary and Ocean Science Center..."

#MicroSky important and thought-provoking 🧵 on the constraints of bacterial chromosome architecture

So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu

Help your fellow researchers decide what nvidia GPU to buy for their @nanoporetech.com basecalling needs. github.com/Kirk3gaard/2...

DTU IT is tracking some network issues that seem to also affect the #antiSMASH servers. I'll post an update once I know more.

Interested in engineering streptomycetes? Struggling with existing genome engineering tools? Then check out our newest paper on CASCADE-Cas3 based genome engineering in streptomycetes! Some highlights below:

Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them? If so, you might this little project: github.com/rrwick/conda...

Now might be a good time to protect your data if you’ve used this service. www.bbc.com/news/article...

NCBI BLAST is down.

everybody heed this pro-tip 👇 from @laurawilliams.bsky.social and, when collecting citations, better make sure to 𝗮𝗹𝘀𝗼 𝘀𝗮𝘃𝗲 𝘁𝗵𝗲 𝗗𝗢𝗜 for the time being, besides PMID/PMC. as of today, none of the >1 k links to PubMed in our blog work ("not found"). we regret the inconvenience.

The NIH website, including NCBI, GenBank, and BLAST are down. I thought it might be a brief outage so waited 12 hours and checked again before posting this. They’re still down. It is hard to express just how fundamental these tools are to biology and medicine: research, applied, public and private.

Roche Xpounds on New Sequencing Technology My deep dive on this exciting new entrant omicsomics.blogspot.com/2025/02/roch... 🧬🖥️

See our latest review about design trends, use, and limitations of Synthetic communities for plant health.

Landmark paper claxon! 'Evaluating the economic and health impact of proactive genomic epidemiology in a hospital setting' www.medrxiv.org/content/10.1... Significant savings associated with proactive genomic epidemiology.

Dorado v0.9.1 now includes a bacterial model for genome polishing, so I put it to the test! How does it compare to Medaka? And does move-table data improve polishing accuracy? Read my analysis here: rrwick.github.io/2025/02/07/d...

Dot plots are an effective (if old school!) way to visualise the pairwise comparison of genomes. For our recent pangenomics project (rdcu.be/d8PZ7), I wrote a small Python package to produce publication ready dot plots. Check it out! github.com/drboothtj/do... pypi.org/project/dotp... 🧪🧬🦠

See the numerous positions at Novonesis on bacterial and fungal strain development - in 🇩🇰 www.novonesis.com/en/careers/j...

Interested in microbial #metabolism, #mucosalbiology and #UTI? Then check out the open postdoctoral position in the Mucosal Immunology Group at ETH Zurich! NB: All applications must go via the ETH job portal: www.jobs.ethz.ch/job/view/JOP... Closing date: 24th Feburary 🧪🧫🔬

Huge performance update in today’s dorado v0.9.1 release on Ampere 8.6/8.7 & Ada Lovelace 8.9 nvidia GPUs with up to 2x increase in throughput with hac calling and 3x sup! 🚀 Plus a whole bunch of updates for dorado polish and the odd misc bug fix. github.com/nanoporetech...

getphylo is finally official! Build phylogenetic trees directly from genbank files - at breakneck speed! I'd like to thank everyone who provided feedback and encourage you to continue. Improving getphylo doesn't stop now the paper is out! 1/5 🧪 bmcbioinformatics.biomedcentral.com/articles/10....

Have a look at @thombooth.bsky.social's #getphylo tool to build phylogenies! Thanks to @thombooth.bsky.social, Simon Shaw, @wemakemolecules.bsky.social (Pablo Cruz Morales) for the great collaboration @dtu.dk!

Has anyone seen this pattern before? @nanoporetech.com 10.4.1 flowcell (severely over warrenty..) on new #Mk1D. Pores get zapped at the first mux scan, and the remaining pores sequence at 200bps instead of 400bps, despite target temp? (also how can there be more failed reads than total reads?)

"Institut Pasteur has decided to leave X because of serious abuses observed on the platform... oppose[s] the campaign by Musk to weaken democracies and destabilize Europe's institutional foundations" www.pasteur.fr/en/home/pres...

4/4 Thanks to my new colleagues @dalofa.bsky.social and @tuesparholt.bsky.social for helping me resolve the tricky terminal inverted repeats in Streptomyces sp. NL15-2K

Feeding 9 billion people will take lots of creativity and the best scientists. Check how Dr. Loes van Dam is working on new fungal foods are DTU biosustain. #DTU_BRIGHT www.euronews.com/health/2025/...