Aaron Pomerantz

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

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

Hi Steven, here are a few that may be helpful -

The nanoMDBG study has some nice comparative datasets www.biorxiv.org/content/10.1...

Ultra-deep long-read metagenomics of soil microbes (used R9)
www.biorxiv.org/content/10.1...

Gut bacteriophage metagenomics pmc.ncbi.nlm.nih.gov/articles/PMC...

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...

#phagesky #phage #microsky

www.biorxiv.org/content/10.1...

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!

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...