Aaron Pomerantz
@aaronpomerantz.bsky.social
Associate Director, Global Segment Marketing @ Oxford Nanopore Technologies - Microbiology, Infectious Disease, Synthetic Biology. The coolest discoveries are the ones you make. Tweets/views are my own.
Reposted by Aaron Pomerantz
Reposted by Aaron Pomerantz
Yeast genomes show how large genomic variations affect trait diversity. #YeastGenomes #GenomicVariations #TraitDiversity #LongReads #Sequencing #Pangenome @nature.com 🧬 🖥️
www.nature.com/articles/d41...
www.nature.com/articles/d41...
October 18, 2025 at 7:05 PM
Yeast genomes show how large genomic variations affect trait diversity. #YeastGenomes #GenomicVariations #TraitDiversity #LongReads #Sequencing #Pangenome @nature.com 🧬 🖥️
www.nature.com/articles/d41...
www.nature.com/articles/d41...
Reposted by Aaron Pomerantz
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-...
September 18, 2025 at 11:12 AM
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-...
Reposted by Aaron Pomerantz
🚨 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
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
September 12, 2025 at 3:34 PM
Reposted by 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...
www.medrxiv.org/content/10.1...
July 30, 2025 at 2:11 AM
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...
www.medrxiv.org/content/10.1...
Reposted by Aaron Pomerantz
🧵🦠🖥️🧬🧪
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/
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
June 25, 2025 at 8:06 PM
🧵🦠🖥️🧬🧪
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/
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/
Reposted by Aaron Pomerantz
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...
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...
June 23, 2025 at 1:01 PM
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...
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...
Reposted by Aaron Pomerantz
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
June 19, 2025 at 8:39 PM
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...
Reposted by Aaron Pomerantz
Francisella tularensis identified using @articnetwork.bsky.social SMART-9N metagenomics and @nanoporetech.com sequencing. Amazing work!
🚨 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/...
wwwnc.cdc.gov/eid/article/...
June 19, 2025 at 10:27 AM
Francisella tularensis identified using @articnetwork.bsky.social SMART-9N metagenomics and @nanoporetech.com sequencing. Amazing work!
Reposted by Aaron Pomerantz
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
June 23, 2025 at 1:04 PM
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
Reposted by Aaron Pomerantz
Very cool!
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
June 19, 2025 at 9:59 PM
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...
June 16, 2025 at 6:53 PM
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...
Reposted by Aaron Pomerantz
New metagenome assembler for ONT R10 and PacBio HiFi reads, from Jim Shaw. See Jim's thread for details
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-docs.github.io
myloasm - metagenomic assembly with (noisy) long reads
myloasm-docs.github.io
May 28, 2025 at 7:07 PM
New metagenome assembler for ONT R10 and PacBio HiFi reads, from Jim Shaw. See Jim's thread for details
Reposted by Aaron Pomerantz
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 🧵.
May 25, 2025 at 10:27 AM
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 🧵.
Reposted by Aaron Pomerantz
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
May 22, 2025 at 10:57 AM
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...
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
First, we saw how the technology continued to advance research in 2024 with ~2/3 of ONT publications in micro/infectious #nanoporeconf
May 23, 2025 at 11:08 PM
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
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!
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
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
May 19, 2025 at 1:53 AM
This is going to be an incredible resource for the microbiology community!
Reposted by Aaron Pomerantz
High-quality metagenome assembly from nanopore reads with nanoMDBG https://www.biorxiv.org/content/10.1101/2025.04.22.649928v1
April 25, 2025 at 12:46 AM
High-quality metagenome assembly from nanopore reads with nanoMDBG https://www.biorxiv.org/content/10.1101/2025.04.22.649928v1
Reposted by Aaron Pomerantz
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
High-quality metagenome assembly from nanopore reads with nanoMDBG https://www.biorxiv.org/content/10.1101/2025.04.22.649928v1
April 25, 2025 at 8:06 PM
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
Reposted by Aaron Pomerantz
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.🙃
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.🙃
April 19, 2025 at 11:24 AM
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.🙃
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.🙃
Reposted by Aaron Pomerantz
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...
www.biorxiv.org/content/10.1...
April 19, 2025 at 2:31 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Aaron Pomerantz
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...
www.biorxiv.org
April 18, 2025 at 9:54 PM
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
Reposted by Aaron Pomerantz
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
February 3, 2025 at 4:32 PM
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.
Reposted by Aaron Pomerantz
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
December 19, 2024 at 5:55 PM
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...