It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.nature.com/articles/s41...

The planktonic microbiome of the Great Barrier Reef - Nature

The Great Barrier Reef Microbial Genomes Database compiles prokaryotic, viral and eukaryotic genomes from seawater collected from the Great Barrier Reef, providing a rich resource for the study of mar...

nature.com

Join Jim Shaw at #ASMicrobe to uncover how to unlock high-resolution, strain-level microbiome insights. Learn how this is could be crucial to helping deliver more precise diagnostics and treatment in the future. https://bit.ly/4v4XuKE

Excited to speak at ASM Microbe 2026 in the Oxford Nanopore session about new tools for long-read metagenomics + 16S sequencing. If you're attending ASM Microbe June 4-7 in D.C. and want to chat, let me know!

Oxford Nanopore@nanoporetech.com · 2mo ago

Join Jim Shaw at #ASMicrobe to uncover how to unlock high-resolution, strain-level microbiome insights. Learn how this is could be crucial to helping deliver more precise diagnostics and treatment in the future. https://bit.ly/4v4XuKE

Our nature note with @philtorres.bsky.social @aaronpomerantz.bsky.social et al. in @ecol-evol.bsky.social was featured in @science.org #ScienceShots written by @sahasmehra.bsky.social #Cyclosa #decoy #spiders #evolution #Peru #Philippines

Science Magazine@science.org · 9mo ago

For the first time, scientists have documented an unusual defense: Some species of arachnids build giant doppelgängers on their webs, creating a frightening deception that scares off would-be killers. https://scim.ag/487Myn0

Congrats @philtorres.bsky.social and @aaronpomerantz.bsky.social on the paper! I look for these decoy spiders whenever I’m in the rainforest and this is the best example I’ve found. #inverts Cuyabeno Reserve, Ecuador 2022

Science Magazine@science.org · 9mo ago

For the first time, scientists have documented an unusual defense: Some species of arachnids build giant doppelgängers on their webs, creating a frightening deception that scares off would-be killers. https://scim.ag/487Myn0

#phagesky #phage #microsky www.biorxiv.org/content/10.1...

Rolling out plaque-2-sequence: a single plaque sequencing approach enabling rapid, low-cost sequencing of phages directly from plaques

Rapid, accurate, and scalable sequencing of bacteriophage genomes is critical to advance phage therapy, build phage biobanks and understand phage genomic diversity. Current methods are based on sequen...

biorxiv.org

Yeast genomes show how large genomic variations affect trait diversity. #YeastGenomes #GenomicVariations #TraitDiversity #LongReads #Sequencing #Pangenome @nature.com 🧬 🖥️ www.nature.com/articles/d41...

Introducing our new Microbial Amplicon Barcoding Kit, which enhances microbial community profiling with an information-rich, rapid & accessible protocol for streamlined identification of bacteria, archaea & fungi — in one go. nanoporetech.com/news/oxford-...

🚨 New tool for viral genomics! Meet CLAE: a high-fidelity Nanopore sequencing strategy that pushes accuracy to Q30, boosts throughput >800 Mb/100 pores, and recovers full-length viral genomes from complex samples 🌊🦠 👉 [https://doi.org/10.1002/advs.202505978] #viromics #nanopore #genomics

Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1 www.medrxiv.org/content/10.1...

🧵🦠🖥️🧬🧪 Please RePost 🙏 We just released reference genomes for another 250 strains to the ATCC Genome Portal (genomes.ATCC.org)! We now have assemblies for _5,750 microbial genomes_ AND all assemblies w/ @nanoporetech.com data will include DNA methylation profiles too (details👇) #genomics 1/

We’re bringing #ASMMicrobe 2025 to you, virtually. Join Robert James, Angela Hickey, and Jose Alexander as they share how real-time, Oxford Nanopore sequencing is transforming microbiology—from single bacterial isolates to the complexities of the microbiome. nanoporetech.com/about/events...

Need bacterial DNA methylation data? Well, we’ve been re-basecalling all ONT data for the ATCC Genome Portal to get it. A huge effort, but as of today we have Mthyl data for ~1,500 bacterial strains. Attending #ASMicrobe? happy to chat IRL about it too. i.e. > genomes.atcc.org/genomes/67e8...

Francisella tularensis identified using @articnetwork.bsky.social SMART-9N metagenomics and @nanoporetech.com sequencing. Amazing work!

Anna (Ganna) Kovalenko@annakovalenko.bsky.social · last yr.

🚨 Tularemia mystery solved in stranded belugas in Alaska! thanks to smart-9N metagenomics & nanopore sequencing 🔬🐋 #wildhealth #onehealth Well done @bortz-virology.bsky.social and Team!! wwwnc.cdc.gov/eid/article/...

What a great key note presentation from @mariechattaway.bsky.social looking at the evolution of #AMR in #Salmonella over the lifetime of #publichealth surveillance. If you enjoyed Marie's talk, then there are many posters featuring work from others @ukhsa.bsky.social's surveillance team here at #I3S

Very cool!

Jonathan Jacobs@bioinformer.bsky.social · last yr.

Need bacterial DNA methylation data? Well, we’ve been re-basecalling all ONT data for the ATCC Genome Portal to get it. A huge effort, but as of today we have Mthyl data for ~1,500 bacterial strains. Attending #ASMicrobe? happy to chat IRL about it too. i.e. > genomes.atcc.org/genomes/67e8...

Each year at @asm.org I'm blown away by the growing amount of presentations and posters leveraging @nanoporetech.com. This year we identified nearly 100 abstracts, ranging from clinical micro & public health applications to environmental research. See you there! nanoporetech.com/about/events...

New metagenome assembler for ONT R10 and PacBio HiFi reads, from Jim Shaw. See Jim's thread for details

Jim Shaw@jimshaw.bsky.social · last yr.

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

Short-read metagenomic sequencing cannot recover genomes from many abundant marine prokaryotes due to high strain heterogeneity and platform-inherent GC bias (likely viruses, too), but Nanopore long reads can address this. A results thread on our recent preprint 🧵.

Steven Robbins@stevenjrobbins.bsky.social · last yr.

Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.biorxiv.org/content/10.1...

Absolutely thrilled to announce the launch of ARTIC2 - a £5.5M 5 year project funded by @wellcometrust.bsky.social to build on the ARTIC approach of low-cost, globally accessible genome sequencing for surveillance of outbreaks, epidemics and endemic diseases: www.birmingham.ac.uk/news/2025/am...

Ambitious project to develop low-cost genome sequencing for pathogens known and unknown - University of Birmingham

Project will build on research that helped diagnostic labs to adopt sequencing capacity for COVID-19 and permit characterisation of future infectious threats

birmingham.ac.uk

Every year there so many amazing @nanoporetech.com updates at London Calling. Here I'll focus on some of my top picks for Microbiology & Infectious Disease 🦠 First, we saw how the technology continued to advance research in 2024 with ~2/3 of ONT publications in micro/infectious #nanoporeconf

This is going to be an incredible resource for the microbiology community!

Jonathan Jacobs@bioinformer.bsky.social · last yr.

Who has DNA methylation from ~5,000 microbes sequenced with @nanoporetech.com? We do. Who’s going to be working their tails off trying to get this data out before ASM Microbe? We are. 🙃 Stay tuned! Major updates coming to the ATCC Genome Portal starting w/methylation data on 1000’s of microbes

High-quality metagenome assembly from nanopore reads with nanoMDBG https://www.biorxiv.org/content/10.1101/2025.04.22.649928v1

It's been a good month for Nanopore assembly preprints! This time metagenomic assembly with nanoMDBG: hundreds of high-quality MAGs from high-complexity communities

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · last yr.

High-quality metagenome assembly from nanopore reads with nanoMDBG https://www.biorxiv.org/content/10.1101/2025.04.22.649928v1

One thing I’m looking forward to this year: Updating the ATCC Genome Portal to be able to deliver the DNA methylation data we have on over 5,000 bacteria and fungi… We just finished rebasecalling all of the raw @nanoporetech.com data we’ve produced since 2019 with the latest version of Dorado.🙃

This new Hifiasm --ont option is amazing. It worked like a charm for us in the nanopore adaptive sampling based assembly paradigm we introduced in a preprint recently. www.biorxiv.org/content/10.1...

Adaptively integrated sequencing and assembly of near-complete genomes

Recent advances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals, plants and other eukaryotes. However, there...

biorxiv.org

Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...

Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...

Efficient near telomere-to-telomere assembly of Nanopore Simplex reads

Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads w...

biorxiv.org

First genome sequence from the Ugandan Ebolavirus outbreak with analysis: virological.org/t/990 and first filovirus genome submitted to Pathoplexus database: pathoplexus.org/seq/PP_0011C.... Great (and rapid) work from the National Health Laboratory, UVRI and partners.

Near Real-Time Genomic Characterization of the 2025 Sudan Ebolavirus Outbreak in Uganda’s Index Case: Insights into Evolutionary Origins

Introduction Case History: On January 30, 2025, the Ministry of Health declared an outbreak of Sudan Ebola Virus (SUDV) Disease in Kampala, Uganda, following the death of a healthcare worker at Mula...

virological.org

Check out our new Apps Note on metagenomic assembly of the Zymo fecal reference with nanopore sequencing and metaMDBG. Almost 200 Gb of metagenomic sequence data from a single PromethION flowcell, yeilding hundreds of high-quality metagenome assembled genomes: nanoporetech.com/resource-cen...

Application note: Oxford Nanopore sequencing provides superior MAG recovery and strain-level resolution from a complex microbiome | Oxford Nanopore Technologies

In this application note, we demonstrate the capabilities of Oxford Nanopore metagenomics by sequencing and analysing the well-characterised ZymoBIOMICS Fecal Reference.

nanoporetech.com