When PCR Gives You Lemons... A Danish group has peered into PCR artifacts and turned them into a fascinating way to index genome libraries omicsomics.blogspot.com/2026/08/when...

Great write-up on the work my colleague Xinglin has been doing.

Keith Robison@omicsomics.bsky.social · 3d ago

When PCR Gives You Lemons... A Danish group has peered into PCR artifacts and turned them into a fascinating way to index genome libraries omicsomics.blogspot.com/2026/08/when...

Follow-up to my last two blog posts: I now look at methylation calling with Dorado v2 and the new hac@v6.0.0 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...

Barbell reveals and resolves demultiplexing and trimming issues in Nanopore data

AbstractMotivation. Oxford Nanopore sequencing enables long-read analysis for diverse applications, but artefacts introduced by Nanopore barcoding are poor

academic.oup.com

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

Microbial QC Survey

A standalone Streamlit app that collects community priority weights over fourassembly-QC metrics ...

microbial-qc-survey.streamlit.app

New blog post! I analyse the new hac@v6.0.0 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?

Claude

Claude is Anthropic's AI, built for problem solvers. Tackle complex challenges, analyze data, write code, and think through your hardest work.

claude.ai

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...

Magdalena Skipper@magdalenaskipper.bsky.social · 2mo ago

Landmark cancer trial shows success against pancreatic cancer, often described as undruggable. The experimental drug, daraxonrasib, disarms all three members of the RAS family of proteins, which are notoriously difficult to target #MedSky 🧪 www.nature.com/articles/d41...

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! 🌎

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 2mo ago

The origin and evolution of archaeal Borg extrachromosomal elements https://www.biorxiv.org/content/10.64898/2026.05.22.727314v1

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.

Kenneth Loi@kenjmloi.bsky.social · 3mo ago

Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.

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

Quanta Magazine@quantamagazine.org · 4mo ago

A powerful electrical motor propels bacteria in virtually every gut and puddle on Earth. After 50 years, it has finally been understood. @nattyover.bsky.social reports: www.quantamagazine.org/what-physica...

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"

Sebastian Schmidt@tsbschm.bsky.social · 4mo ago

This simulation-cum-benchmark study on MAG making by @tkorem.bsky.social & team looks really interesting. Loads of plots and results to work through! www.biorxiv.org/content/10.6...

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

ONT nesting material

YouTube video by Graham Etherington

youtu.be

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...

151 - Deacon part 1

In this Software Deep Dive episode, we talk with Dr. Bede Constantinides (University of Birmingham) about Deacon, a tool for removing host DNA reads from metagenomic datasets. We discuss why host read

soundcloud.com

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...

Convergent extreme reductive evolution in ancient planthopper symbioses - Nature Communications

Symbiotic bacteria can have exceedingly small genomes. This study finds that ancient bacterial symbionts of planthoppers have repeatedly evolved the smallest known genomes, losing most biosynthetic fu...

nature.com

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...