Matt Parker
@bioinfomatt.bsky.social
Director, Clinical Bioinformatics Software at Oxford Nanopore in the EPI2ME team. Interested in regulated application of Nanopore sequencing. Also bikes, beers, trains, and the American Office.
One thing I didn’t appreciate until London Calling this year is that @nanoporetech.com is now releasing more technical documentation and datasets as blog posts.
Mike Vella@vellamike.bsky.social · last yr.In this blog post, we show how chromatin accessibility can be profiled with minimal processing using nanopore sequencing – preserving native structure and capturing rich signal. Read it here: epi2me.nanoporetech.com/chromatin-ac...
New blog post! In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup. Check it out for the full results: rrwick.github.io/2025/05/27/d...
Dorado v1.0.0 and the v5.2.0 basecalling models
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
The @nanoporetech.com #EPI2ME team is hiring! If you want to build workflows to analyse @nanoporetech.com sequencing data for end to end applications then this job is for you! ejnh.fa.em2.oraclecloud.com/hcmUI/Candid...
Bioinformatics Software Developer
We are looking for talented Bioinformatics Software Engineer to work within the Customer Analysis Workflows group who will be responsible for developing coherent bioinformatic software tools for end u...
ejnh.fa.em2.oraclecloud.com
Exciting preprint from Haoyu Cheng (not on bluesky?) and @lh3lh3.bsky.social: building amazing Nanopore assemblies just got faster and more accessible! Thrilled to have played a small part in this work!
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · last yr.Efficient near telomere-to-telomere assembly of Nanopore Simplex reads https://www.biorxiv.org/content/10.1101/2025.04.14.648685v1
Missed our knowledge exchange on Oxford #Nanopore comprehensive metagenomic sequencing for pathogen surveillance? Watch the recording here! buff.ly/IDhJt0S This approach allows for discovery of #bacteria, #fungi, and viruses directly from respiratory samples #metagenomics #viromics
Metagenomics for pathogen surveillance
In this webinar, we learn how Oxford Nanopore sequencing can provide a rapid and comprehensive metagenomic approach for characterising bacteria, fungi, and viruses directly from respiratory samples.
nanoporetech.com
New version of Oxford @nanoporetech.com Dorado v0.9.5
Chris Seymour@iiseymour.bsky.social · 2y agoHuge performance update in today’s dorado v0.9.1 release on Ampere 8.6/8.7 & Ada Lovelace 8.9 nvidia GPUs with up to 2x increase in throughput with hac calling and 3x sup! 🚀 Plus a whole bunch of updates for dorado polish and the odd misc bug fix. github.com/nanoporetech...
Peter Marks’s resignation letter. Everyone should read this.
Less than two months to @nanoporetech.com London calling. Anyone secretly testing new pores? Kit chemistry? Devices?
This week we celebrated 20 years of innovation! To mark the occasion, we’re offering 20 complimentary in-person tickets to London Calling for researchers facing barriers to attendance. Apply here: share.hsforms.com/1rfrIYeGhTCG... #nanoporeconf
#AGBT2025 #AGBTGM has been incredible. Lucky to be part of the event with @nanoporetech.com - as always we were so looked after by our amazing events team! (Photo credit to @minomatt.bsky.social)
Stop by the @nanoporetech.com Lanai suite #190 at #AGBT2025 #AGBTGM tonight after the welcome reception. We’re open from 7pm. We can’t wait to PORE you a beverage. 😂
Landmark paper claxon! 'Evaluating the economic and health impact of proactive genomic epidemiology in a hospital setting' www.medrxiv.org/content/10.1... Significant savings associated with proactive genomic epidemiology.
Recent #birdflu cases highlight the need for proactive #pathogen monitoring. Read how researchers using nanopore sequencing in wastewater detected surges in #influenza A, showing its potential as an early warning system. Read here: www.the-microbiologist.com/news/sewage-... #H5N1
Sewage could act as early warning system for influenza A outbreaks
Researchers monitoring wastewater for avian and human influenza A virus have detected a surge in virus as the flu season got underway, showing that the technique could act as an early warning system f...
the-microbiologist.com
My 1st “computer” - I remember that genesis motherboard being very in the way when we tried to upgrade the RAM!
KevFun Newburn@kevinnewburn.bsky.social · 2y agoOne of my favorite oddball formats the Sega Genesis found itself in was the Amstrad Mega PC. A 386sx PC that also had an entire genesis motherboard on a ISA card. I'm fascinated by this sort of console/pc hybrid concept.
Join us next week for a webinar on 🧬nanopore sequencing 🧬 featuring speaker Stephanie Chrysanthou of MSK Cancer Center. Learn about the fundamentals, applications and impacts — and earn CE/CMLE credits. educate.amp.org/local/catalo...
There were remarkable updates presented at #PAG32 on incredibly accurate @nanoporetech.com sequencing for applications ranging from telomere-to-telomere plant & animal genome assemblies, to amplicon sequencing at massive scale. Here are some highlights in case you missed them (thread)
CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-025-06036-0 🧬🖥️🧪 #Rstats https://github.com/gmoro-bioecopest/CompareGenome
Following the announcement of our first speaker Jeff Nivala, we’re happy to announce early bird tickets for London Calling 2025, are now available. Make sure to purchase before 19th Jan to avoid the price increase. Get your ticket here: nanoporetech.com/about/events... #nanoporeconf
London Calling 2025
London Calling - Oxford Nanopore's annual conference
nanoporetech.com
Oxford Nanopore@nanoporetech.com · 2y ago1/ We’re excited to announce our first speaker of London Calling 2025 Jeff Nivala will share their groundbreaking ‘proof-of-concept' method showcasing the capability of #nanopore sequencing to read #polypeptide strands. Register here: nanoporetech.com/about/events... #nanoporeconf
1/ We’re excited to announce our first speaker of London Calling 2025 Jeff Nivala will share their groundbreaking ‘proof-of-concept' method showcasing the capability of #nanopore sequencing to read #polypeptide strands. Register here: nanoporetech.com/about/events... #nanoporeconf
Oxford @nanoporetech.com 2024 results: - Commercial performance accelerated in the second half in-line with guidance; underlying revenue growth in the second half was approximately 34% on a constant currency basis
Our research this year covered: 🔬 TB diagnostics and technological innovations 💉 TB vaccines and preventive strategies 💊 Drug resistant #TB (DR-TB) and treatment innovations 🙌 Post-TB care and person-centred approaches 💸 Economic and #PublicHealth impacts of TB Find them here:
KNCV Publications - KNCV - Tuberculosefonds
On this page you can find the up-to-date list of KNCV publications, research conducted within KNCV and partner organizations.
kncvtbc.org
Merry Christmas! Smoked port old fashioned to finish me off 🥂
Due to the limitations of short read sequencing, this mutation has remained hidden for more than 25 years since ASPA mutations were first characterized in individuals Canavan disease. 2/
I gave the @seqera.io @nextflow.io AI the challenge of writing me a workflow that produced a really grumpy Christmas message. Damn guys - what you been feeding this thing??
New release of Canu - first one in over 3 years! github.com/marbl/canu/r... The notes say this will be the very last release. Many thanks to its devs Brian Walenz and @sergek.bsky.social. Canu may be a bit old and it's certainly not fast, but it makes good assemblies and so I still use it!
Release Canu v2.3 · marbl/canu
These are release notes for Canu version 2.3, which was released on December 17th, 2024. Canu is specialized for assembly of single-molecule sequences. Full documentation can be found at http://can...
github.com
