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PolyA tail lengths can be accurately estimated using Nanopore dRNA

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We have developed workflows for Plasmid precursor quality control

Oxford Nanopore simplifies RNA QC in GMP

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GMP QC is laborious and complex

mRNA shows huge promise in personalised cancer vaccines

Next up - Chris Alder discusses QC workflows in biopharma

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New for 2025 in EPI2ME - Teloseq, trio and pharmacogenomics workflows

Single cell workflows now adds the ability to detect gene fusions

EPI2ME workflows are next flow based you can upload your own

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2ME format allows users to share workflows offline - code available on GitHub

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EPI2ME free to download and runs on Windows, Mac and Linux

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Sarah Grifftihs next up with updates on EIPI2ME

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We observe SOTA results in INDEL F1 scores for GIAB benchmarks, particularly big improvements in long INDELs

Dorado variant is a completely new architecture - not a port of an existing variant caller

Dorado v1.0.0 includes a preview release of our very own variant caller

Dorado polish goes hand in hand with hifiasm- >2Q improvement to assemblies

Dorado polish uses much more information than before, leading to higher quality assembly polishing.

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LSK-only Nanopore reads able to produce 23 gapless chromosomes , 10 scaffolded, and N50>130Mb

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Huge strides have been made in assembly. Nanopore-only T2T assembly is now feasible and will soon be routine.

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Many ways of answering the question “what is the genotype of my sample?”

Up next - @rwinds.bsky.social discusses the latest in variant calling and assembly

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Base calling obeys scaling laws in deep learning - a Q28 base caller using standard chemistry is now available on demand.

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Base calling accuracy is compute-limited. As GPUs get faster so does accuracy!

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Dorado v1.0.0 introduces dramatic improvement to modified base calling speed

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Big improvements in modification calling accuracy - 6mA increases from Q16 to Q24

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New HAC models are 1.4Q more accurate - a 25% error reduction

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Dorado is no longer “just” a base caller - now includes alignment, mod base calling, alignment, and now even variant calling

Ryan Wick @rrwick.bsky.social · 21/02/2025

First up, @iiseymour.bsky.social with updates on all the new features in Dorado

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Reposted by Mike Vella

I re-ran previous ONT basecalling benchmarks using the latest version of Dorado (thanks, @vellamike.bsky.social), and the RTX 40 series GPUs show an impressive speed boost! Check out the updated benchmark results at the bottom of this post: rrwick.github.io/2024/08/16/s...

rrwick.github.io

Spring OnION: a high-spec laptop for ONT sequencing

a blog for miscellaneous bioinformatics stuff

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Mike Vella @vellamike.bsky.social · 20/02/2025

Dorado now supports bacterial genome polishing. It can output assemblies in FASTQ, including Q scores. @rrwick.bsky.social 's analysis shows Q scores are well correlated with base call reliability, meaning they can help reduce false positives in variant calling. rrwick.github.io/2025/02/19/f...

rrwick.github.io

FASTQ assemblies with Dorado polish

a blog for miscellaneous bioinformatics stuff

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Reposted by Mike Vella

Rhydian Windsor @rwinds.bsky.social · 17/12/2024

Awesome to see the assembly polishing models we've been working on the last couple of months finally out there - we've had some really promising results with these internally so keen to see how others get on with them!

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Mike Vella @vellamike.bsky.social · 17/12/2024

🎄 New Dorado release (v0.9.0) – and it's big! 🚀 Dorado polish command (experimental) for improving draft assemblies – faster & more accurate than Medaka ⚡ Faster modified base calling models 🔧 Usability & accuracy improvements: PolyA, Barcoding, 6mA calling github.com/nanoporetech...

github.com

Release v0.9.0 · nanoporetech/dorado

[0.9.0] (16 Dec 2024) This major release of Dorado introduces several new features and enhancements. The polish command, currently experimental, is optimised for refining draft assemblies of human ...

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Reposted by Mike Vella

Matt Loose @minomatt.bsky.social · 28/11/2024

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!

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Reposted by Mike Vella

Oxford Nanopore @nanoporetech.com · 22/11/2024

Excited to join the #Nanopore Community on BlueSky. Follow us for the latest updates and discussions about Oxford Nanopore and Nanopore Community. #WYMM

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Mike Vella @vellamike.bsky.social · 23/11/2024

At @nanoporetech.com, we've used ML to achieve remarkable advancements in basecalling. Now, we're focusing on driving further improvements in consensus and variant calling, enhancing both speed and accuracy. Watch @rwinds.bsky.social update on our progress: www.youtube.com/watch?v=IB6D...

youtube.com

Secondary analysis update

YouTube video by Oxford Nanopore Technologies

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Mike Vella @vellamike.bsky.social · 14/11/2023

Just released an update to ONT's basecaller Dorado (version [v0.4.3]) : 🧬 🖥️ * m6A DRACH-context mod model * poly(A) / poly(T) tail estimation * RNA read splitting * RNA adapter trimming Plus sample sheet support * Significant memory reduction for duplex calling. github.com/nanoporetech...

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Mike Vella @vellamike.bsky.social · 05/11/2023

This paper is amazing. Using Oxford Nanopore sequencing in CNS tumor diagnostics is a remarkable example of engineering meeting clinical innovation. Our work on accurate GPU-accelerated basecalling has helped enable sample-to-sequence, with methylation, swiftly. www.nature.com/articles/s41...