Aaron Pomerantz

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!

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!

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

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 🧵.

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

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...

Hope you enjoyed this London Calling 2025 #NanoporeConf recap. As always, it's the people - my colleagues and the community - who make all of this possible and drive the field forward, even in challenging times

Last but certainly not least, we're taking these applications beyond research into applied industries & biopharma, including plasmid, AAV, mRNA manufacturing and adventitious viral agent contamination, provider deeper insight & faster TAT for these critical biological materials

Direct RNA sequencing is also coming into the limelight for micro, highlighted by Chloé Baum at Pasteur Institute with dengue & chikungunya. Now with 24 barcodes coming for direct RNA multiplexing, this will become a critical tool for novel insights without biases of cDNA

Bonus post sneaking in eukaryotes! High-quality, telomere-to-telomere (T2T) assemblies have potential to set a new gold standard, but were challenging & resource intensive. That's now changing thanks to new software like hifiasm-ONT - check out these amazing assemblies in 🐝🌽🐮

I also believe that the next frontier is Microbial Epigenomics. Detection of base modifications is best-in-class with @nanoporetech.com & the data is already right there every time you sequence a microbial sample directly without PCR. What discoveries are lurking right under our noses?

This extends beyond microbial isolates into complex microbiomes. @sisseljuul.bsky.social and @dorylophile.bsky.social showcased beautiful benchmarking data on superior genome recovery and strain-level resolution in the ZymoBIOMICS Fecal Reference with ONT compared to alternative sequencing platforms

The ability to resolve closed microbial genomes & plasmids has been a critical case for long-reads, but our teams have been pushing to make ONT all you need - thanks to updates in basecalling/polishing, you now get best of both worlds: high-quality assemblies with high-accuracy

bsky.app/profile/nano...

Michael Wiley from Nebraska Public Health shared his great experience with the ElysION device on automated sample-to-answer microbial isolate WGS for hospital-acquired infections, finding that ONT served as a faster, cost-effective, accurate platform to support HAI investigations

bsky.app/profile/nano...

Our community members presented incredible ONT use cases, including Judith Breuer showcasing how rapid metagenomics is faster than standard microbiology for identifying respiratory infections & how new targeted methods increase sensitivity & speed for sterile sites www.medrxiv.org/content/10.1...

One of the new kits I am personally very excited about is the Microbial Amplicon Barcoding Kit - a library prep approach for fast, flexible, full-length amplicon sequencing. If interested, please check out our registration page while we ramp production register.nanoporetech.com/microbial-am...

@rsinclairdokos.bsky.social then highlighted our maturing portfolio of End-to-End solutions in this segment, including full-length 16S/ITS, viral WGS, bacterial & fungal isolate WGS, metagenomics, & synthetic construct verification. You can check out the full tech update youtube.com/watch?v=OYql...

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!

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

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.🙃