Lightnews — Scholar-powered news

Reposted by Aaron Pomerantz

Oxford Nanopore @nanoporetech.com · 21d

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-...

1 4 13

Reposted by Aaron Pomerantz

Sullivan Lab at OSU @sullivan-lab.bsky.social · 26d

🚨 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

1 8 16

Reposted by Aaron Pomerantz

Hugh Cottingham @hughcottingham.bsky.social · Jul 30

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...

3 29 44

Reposted by Aaron Pomerantz

Jonathan Jacobs @bioinformer.bsky.social · Jun 25

🧵🦠🖥️🧬🧪
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/

Home | ATCC Genome Portal

The ATCC Genome Portal is a repository of high-quality, authenticated microbial reference genomes.

genomes.ATCC.org

1 19 31

Reposted by Aaron Pomerantz

Oxford Nanopore @nanoporetech.com · Jun 23

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...

2 3 3

Reposted by Aaron Pomerantz

Jonathan Jacobs @bioinformer.bsky.social · Jun 19

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...

ATCC® 9945a™ | Bacillus paralicheniformis | ATCC Genome Portal

Bacillus paralicheniformis is a strain of bacteria in the Bacillus genus. This genome was published to the ATCC Genome Portal on 2022-04-02

genomes.atcc.org

2 9 30

Reposted by Aaron Pomerantz

Josh Quick @scalene.bsky.social · Jun 19

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

Anna (Ganna) Kovalenko @annakovalenko.bsky.social · Jun 18

🚨 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/...

1 3 9

Reposted by Aaron Pomerantz

Emma Waters @emmabeansworth.bsky.social · Jun 23

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

5 11

Reposted by Aaron Pomerantz

Samuel Lampa @smllmp.bsky.social · Jun 19

Very cool!

Jonathan Jacobs @bioinformer.bsky.social · Jun 19

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...

ATCC® 9945a™ | Bacillus paralicheniformis | ATCC Genome Portal

Bacillus paralicheniformis is a strain of bacteria in the Bacillus genus. This genome was published to the ATCC Genome Portal on 2022-04-02

genomes.atcc.org

1 1 3

Aaron Pomerantz @aaronpomerantz.bsky.social · Jun 16

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...

2 2

Reposted by Aaron Pomerantz

Heng Li @lh3lh3.bsky.social · May 28

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

Jim Shaw @jimshaw.bsky.social · May 28

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

myloasm - metagenomic assembly with (noisy) long reads

myloasm-docs.github.io

13 32

Reposted by Aaron Pomerantz

Steven Robbins @stevenjrobbins.bsky.social · May 25

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 🧵.

1 23 44

Reposted by Aaron Pomerantz

Nick Loman @pathogenomenick.bsky.social · May 22

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

www.birmingham.ac.uk

7 80 230

Aaron Pomerantz @aaronpomerantz.bsky.social · May 23

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

Aaron Pomerantz @aaronpomerantz.bsky.social · May 23

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

1

Aaron Pomerantz @aaronpomerantz.bsky.social · May 23

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

1

Aaron Pomerantz @aaronpomerantz.bsky.social · May 23

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 🐝🌽🐮

1 1

Aaron Pomerantz @aaronpomerantz.bsky.social · May 23

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?

1 1 2

Aaron Pomerantz @aaronpomerantz.bsky.social · May 23

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

1 1 1

Aaron Pomerantz @aaronpomerantz.bsky.social · May 23

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

1

Aaron Pomerantz @aaronpomerantz.bsky.social · May 23

bsky.app/profile/nano...

1

Aaron Pomerantz @aaronpomerantz.bsky.social · May 23

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

1

Aaron Pomerantz @aaronpomerantz.bsky.social · May 23

bsky.app/profile/nano...

Oxford Nanopore @nanoporetech.com · May 23

Robustness and scalability matter in clinical genomics.
Respiratory metagenomics has shown us what’s possible —but to scale, we need a method that’s robust, transferable, and standardised. That’s where Judith Breuer believes Oxford Nanopore comes in: flexible, scalable, and ready to roll out.

1

Aaron Pomerantz @aaronpomerantz.bsky.social · May 23

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...

1 1