Follow-up to my last two blog posts: I now look at methylation calling with Dorado v2 and the new [email protected] model from @nanoporetech.com. rrwick.github.io/2026/07/08/d...

New! R-scape version v2.6.11 github.com/EddyRivasLab... with drawings of R-scape annotated RNA consensus structures with many fewer overlaps!! Using RFview github.com/dincarnato/R... Shout out to @incarnatolab.bsky.social for displaying R-scape's covariation outputs + CaCoFold-R3D structures.

The Barbell paper found ONT technical sequence in 22 of my genomes. The issues are closely linked to the linear topology of Streptomycetes, unusual to assemblers. In the >1000 genomes, I found 35 with 20-200nt ONT tech.seq. All are now corrected, soon to hit the DB. academic.oup.com/bioinformati...

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

For anyone doing ONT Microbial Genomics, please take 1 minute (less?) to tell us which assembly metrics you care most about when evaluating whether an assembly is "good". We are doing a benchmark of different QC tools (barcode/adapter trimming and QC filtering). microbial-qc-survey.streamlit.app

New blog post! I analyse the new [email protected] basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model: rrwick.github.io/2026/06/11/d...

How strange that Claude.ai adds references which stem from previous, completely unrelated prompts, like a Streptomyces reference on an mpox prompt. Anyone else observed/been annoyed by this?

Wonderful progress, and as a #Streptomyces guy, I'm also thrilled to see the complete original sanglifehrin #BGC in the strain Gö40/10 which I've worked with! www.ncbi.nlm.nih.gov/nuccore/NZ_C...

super cool stuff guys!

So, I know birds can swallow large prey. But this was pretty wild. At Yolo Bypass, near LotG, I witnessed a juvenile pied billed grebe catch, struggle with, and then eat a crawfish. And the crawfish, relative to the grebe, was quite big. #birds

Super excited to share the final project of my postdoc career! We found that Borgs and mini-Borgs are widespread across diverse ecosystems. They don't just exist in Banfield Lab — they are everywhere! 🌎

Our study into the incredible genome of Embleya australiensis has been published in Microbial Genomics. We've shown that Embleya carry gigantic secondary chromosomes around 4 - 6 Mb in size! Enjoy reading and don't hesitate to reach out! www.microbiologyresearch.org/content/jour... 🧪💻🦠 1/4

With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...

The nvidia dgx spark is a cool box but you get more @nanoporetech.com basecalling for your money with one of the other options (github.com/Kirk3gaard/2...)

What if multireplicon plasmids are not an oddity, but an evolutionary strategy? We found that they are common, more mobile, broader-host-range, and enriched in AMR. Even more interesting: their assembly doesn’t look random. 👀 Paper preprint: www.biorxiv.org/content/10.6... Thread below!🧵👇

Streptomyces is the most species rich genus in the new GTDB release, and I'm proud that G1034, our big HQ genomes project, contributed almost 200 of the species representatives from that genus alone. gtdb.ecogenomic.org/stats/r232 @kblin.bsky.social @tilmweber.bsky.social

J. Craig Venter, genomics pioneer and founder of JCVI and Diploid Genomics, Inc., dies at 79 www.jcvi.org/media-center...

We present VIPR, a phage-encoded RNA-guided system that recognizes DNA with a noncontiguous code unlike CRISPR. Tiny, programmable, possibly ancestral to CRISPR immunity; VIPR is built around a striking RNA-DNA-DNA triplex.

great article in @quantamagazine.bsky.social by natalie wolchover on the bacterial flagellum and proton motive force. alas, I missed this great model on what happens to the stators during gear-shifting. see it in STC: smallthingsconsidered.blog/schaechter/2... #MicroSky

Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.

Absolute banger: "find that metaSPAdes consistently outperforms MEGAHIT" "Binning refinement, which combines bins from multiple different algorithms, leads to reduced performance" "We further show that CheckM2 systematically overestimates completeness and underestimates contamination"

Excited to share our new findings in @science.org on how the DRT3 bacterial defense system uses a reverse transcriptase that builds DNA repeats without a nucleic acid template. Microbes never cease to amaze! www.science.org/doi/10.1126/...

At @earlhaminst.bsky.social it's always nice to get a brand new @nanoporetech.com flow cell, but in spring it's even better. You can recycle the woollen packaging by putting it into a bird feeder, which birds will use for nesting material. Here's a Blue Tit doing just that. youtu.be/r6b00j0PXRo

This day 86 years ago, Nazi Germany invaded Denmark and the Danish soldiers got orders to surrender. My grandfather and his entire generation preached until their death: Never Again a 9th of April! I hope their plea stays untested 🇬🇱🇩🇰

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...

Eukan: a fully automated nuclear genome annotation pipeline for less studied and divergent eukaryotes academic.oup.com/nargab/artic... 🧬💻🧪 github.com/BFL-lab/eukan

Madness. A bacterium with a 10kb genome, lost replication initiation, translation.., relies on symbiotic host. www.nature.com/articles/s41...

Now out in @natcomms.nature.com : versions 2.0 of both BiG-SCAPE and BiG-SLiCE! With significant speed and accuracy increases, as well as new interactive functionalities. Read the full paper here #openaccess: www.nature.com/articles/s41...

Check out our paper in @asm.org Applied and Environmental Microbiology 🍾 OSMAC guided bioprospecting of Atlantic sponges reveals novel bacterial species and the antimicrobial thiazole alkaloid agrochelin II | Applied and Environmental Microbiology journals.asm.org/doi/10.1128/... #secmet #microsky

Research into filamentous actinomycetes, the antibiotic producers, is in steep decline. Loads of natural products chemistry research worldwide but not much aimed at understanding their biology and ecology. The latter is key to unlocking their specialised metabolism link.springer.com/article/10.1...

Another example of a custom-made 3D-printed 96-well magnet bead purification device, triggered by a "pipette eject" event on the OpenTrons. Essentially, if the OpenTrons is thought as a flexible pipetter, then @plasmidsaurus.bsky.social turn pipette events into other MolBio tasks.

Another interesting use of 3D printed plastic adapters, in this case to turn the OpenTrons bays into racks of Oxford @nanoporetech.com PromethION flowcells.

Time for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]

🦠🧬🖥️ Bakta v1.12.0 is out with tons of tiny improvements and bug fixes, too many to list all: - partial genes on linear seqs - improved errror handlings & runtimes - support Python 3.12 & 3.13 - ... A huge shout out and thank you to all bug reporters and contributors! github.com/oschwengers/...

First fully phased reference genome for the Yarrowia liploytica type-strain is out! academic.oup.com/jimb/advance... Super fun project in collaboration with James Crill at Syracuse University as well. Important platform organism for industrial microbiology and biomanufacturing as well. #genomics

New tool from @alexsweeten.bsky.social to find and classify all your satellites: "AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates" 📄 www.biorxiv.org/content/10.6... 📦 github.com/marbl/anianns

Exploring #microbiome data? MetaTree makes statistically based hierarchical tree comparisons easy and accessible.

My understanding of MDPI as the biggest polluter of science gets some quantitative basis in this cool study. How about we as researchers stop publishing there and stop reading it leaving the special issues with another issue: absence of honest science.

ONT Axes P2 Solo, Roiling Community 🧬🖥️ omicsomics.blogspot.com/2026/01/ont-...

New blog post with some thoughts on @nanoporetech.com and their recent announcement that the P2 Solo will be discontinued: rrwick.github.io/2026/01/21/p...

Ultra-high-throughput mapping of genetic design space www.nature.com/articles/s41... (read free: rdcu.be/eY6E2) 🧬🖥️🧪 github.com/cbashorlab/C...

Unpacking my stuff in my new @ssi-dk.bsky.social office, I came across this post which resonated enough that I printed it out and hung it up on my wall. It's going back up now. I think from @danpsimpson.bsky.social ?

Been doing a lot of @nanoporetech.com sequencing for soil and sediment lately and it appears that no matter how much DNA or how little we still get decent yields. So pretty robust performance. Yield clearly depends on pore count.

Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive. Here we explore the conjugative capacity of these mysterious Genomic Islands. www.biorxiv.org/content/10.6...

I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!

How delightful to start the year with a neat overview of the sequencing field from the most capable watcher of the space.

Sequencing Instrumrnt Outlook 2026 My observations & predictions on sequencing instrument companies 🧬🖥️ omicsomics.blogspot.com/2026/01/sequ...

Staying Current in Data Science and Computational Biology: 2026 Edition. Part 3 in a series of posts going back 14 years. doi.org/10.59350/2na...

New preprint. Work led by @ainsley-beaton.bsky.social & Rebecca Devine. They show the highly conserved Streptomyces MtrAB two component system activates ectoine production and triggers sporulation in response to osmotic stress in Streptomyces venezuelae www.biorxiv.org/content/10.6...

Born #OnThisDay in 1922, Esther Lederberg was the first to isolate the lambda phage in 1951. She characterised the lysogenic phase, whereby the phage are able to integrate into the bacterial genome, staying dormant. This discovery made them a model tool of study, leading to many more breakthroughs.