Very interesting day at the genomics England long read summit. And great to catch up with @generoom.bsky.social and more!

Very nice summary of a number of cohorts and chemistries across @nanoporetech.com from genomics England.

Spent the last hour helping solve quadratic equations for my son’s maths homework. I knew my A-level maths would one day come in useful. And it has. To do his A-level maths.

PhD opportunity available on epigenomics/trasncriptomics as part of the network of clinicians and researchers working in glioblastoma research at @uniofnottingham.bsky.social Using a wide range of tech and methods but definitely long reads @nanoporetech.com - more at lnkd.in/eBtrtZiM

A bit like spiralling publication costs we need to start having a proper discussion around lab equipment servicing costs. These are often completely disproportionate to the cost of instrument and the service that is provided and seem to serve as a cash cow for vendors.

Great to see this paper out www.nature.com/articles/s41... including Chris Moore of the Nottingham DeepSeq team. Chris took @nanoporetech.com Mk1Cs out to Columbia and sequenced chocolate. Coverage www.theguardian.com/science/2025... and institutions.newscientist.com/article/2492....

For @nanoporetech.com geeks I’ve just been pointed at this very helpful site - nanoporetech.github.io/ont-output-s... - I hadn't seen this before and it's very useful!

Really pleased that this paper is out - academic.oup.com/neuro-oncolo... thanks to all our collaborators far and wide who have helped and of course @nanoporetech.com

UK Genome Science meeting - Newcastle. 9th - 11th July 2025. Great speakers. Great community. Early bird registration-16th May Abstract submission-23rd May Registration close-26th June If you want that sweet sweet early bird deal - get going quick! www.genomescience.org.uk

RIP MK1B. You always punched way beyond your weight. @nanoporetech.com about that mk1D…

Faster Brain Tumour classification now being validated in Sydney @lavsat.bsky.social based on the work of @minomatt.bsky.social and collaborators youtu.be/sfykXrvSs28

UK Genome Science 2025 is going live for this year - www.genomescience.org.uk - get registering!

A benefit of being on the other side of the world is being able to watch the sprint race live.

Real pleasure to be presenting at the @nanoporetech.com #WYMM event in Melbourne Australia today. Great to see the pores work equally well upside down. And at last - socks! Though I still think they should be the long sock… youtu.be/zxI-pcLj9XE?...

Just wish I knew what the actual question was… “FASTA, FASTQ and FAST5…” - fill in the blanks?

Great to be visiting @nanoporetech.com as part of a cns Nanopore symposium meeting with pathologists and clinical scientists to discuss the application of nanopore sequencing in the clinic.

No filter.

#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)

Well done @fogenomics.bsky.social another fantastic meeting ✨ Caught up with so many friends 🙏 Great speakers and even better networking 🧬🧬 #FOG2025 See you all in July at Genome Science, in Newcastle 🥳

For info - it’s DeepSeq for all your next generation sequencing needs. Deep Seek will do something completely different…

They said I’d be able to check my accounts more quickly… everything would be simpler. 15 minutes later - I still can’t see how much money is in my account. Could someone at a university tell me that this system gets better over time? Because so far… it’s exactly as bad as people said it would be.

Fun to see some killer whale poo seq on #bbc2 today using @nanoporetech.com Still want to get a whale read from a whale one day!

Happy New Year all!

Well - this is awkward. According to santatracker.google.com Santa is on his way. But according to Norad www.noradsanta.org/en/map he’s going to take off shortly. Something up with norad?

And so we reach the glorious time of year where authors try to push papers to editors to “get them off the desk” whilst editors try to clear their desks for the break. Referees try to rapidly return reports to editors and nothing will happen to anything for a good 10 days…

Nottingham Nanopore contingent out to celebrate Dr Munro

Does cold emailing academics with information on commercial services or products actually work? I find academics very rarely respond to emails let alone cold ones. The worst are the ones that try and guilt trip you into responding…

This is worth looking at. Trying some genomes we have assembled with earlier versions of hifiasm, hifiasm plus herro and then this new version of hifiasm. The early assembly results suggest that now hifiasm alone is equivalent to what we got with herro but with less compute!

Still not resolved.

Saturday. Saturday. Saturday. Saturday. Saturday.

Its interesting to see my PhD students slow and dawning realization that the hardest thing he will ever have to do is submit his data to an online open database…

Given that this place has become a little busier in recent days I’m reposting this. We’re doing a lot of work in this tool at present and it’s great to be working so closely with Nottingham university hospitals.

It’s Friday evening. Any banter happening anywhere?

After editing, this very short letter to New Scientist is even shorter now. But I think it gets the point across! @faecalmatters.bsky.social

Lots been going on in the last few days. Plenty to process and think about.

Bluesky really seems to be taking off in the last few days. Did something happen?

Looks like this place is filling up.

Introducing ROBIN. Rapid nanopOre Brain intraoperatIve classificatioN. ROBIN builds on work by many groups and shows how we could reduce turnaround time for full molecular classification of CNS tumours in NHS clinical settings from weeks to hours. www.medrxiv.org/content/10.1...

Is there more happening here now?

Introducing ROBIN. Rapid nanopOre Brain intraoperatIve classificatioN. ROBIN builds on work by many groups and shows how we could reduce turnaround time for full molecular classification of CNS tumours in NHS clinical settings from weeks to hours. www.medrxiv.org/content/10.1...

Martin’s on a plane with a Danish guy dressed as Darth Vader en route to the US. Unfortunately due to the IT outage his case wasn’t loaded on the plane. Thoughts and prayers to that dude.

Old @pathogenomenick.bsky.social told me that blue sky is the place to be so I thought I’d see if that is true again.

We are holding an event on Thu 27 Jun 10:00 AM - 5:00 PM: CNS Rapid Diagnostics Information Day - this will cover our research only use of nanopore technology in looking at tumours. The meeting is in person and requires registration, but is free to attend. buytickets.at/cnstumourdia...

@pathogenomenick.bsky.social I’ve just looked and you don’t have that many.

Should I use this more?

For a few years I've been thinking about calling somatic mutations without matched normals using long read haplotypes. I've posted a preprint with my experiments to explore when this works (and when it doesn't) and developing a prototype mutation caller ("smrest"): www.biorxiv.org/content/10.1...

Anything happening?

We've put out a new version of readfish, our tool for Nanopore adaptive sampling. This is our v1.0 release and has a lot of improvements, tweaks and stability issues addressed. It has been in testing for a long time and works with all ONT platforms github.com/looselab/rea....

First Apple event I don’t watch live in 20+ years…

Looking at holding a day on Nanopore adaptive sampling in Nottingham. Would discuss use cases, best practice, analysis and specific examples. If you’d be interested reply to this and state if November, Early December, Late Jan or February would be better for you!