Yesterday in Malta the season for Dorado (Lampuki in Maltese) fishing opened, which is fantastic luck for me as I can enjoy a delicious dinner! My favourite basecaller and favourite fish share the same name.
Mike Vella
@vellamike.bsky.social
Head of Machine Learning at Oxford Nanopore, driving fast algorithms and research to analyze DNA/RNA/Proteins.
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...
Chromatin accessibility data and tool release
Functional epigenomics uses high-throughput sequencing data to study how epigenetic modifications…
epi2me.nanoporetech.com
PolyA tail lengths can be accurately estimated using Nanopore dRNA
We have developed workflows for Plasmid precursor quality control
Next up - Chris Alder discusses QC workflows in biopharma
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
2ME format allows users to share workflows offline - code available on GitHub
EPI2ME free to download and runs on Windows, Mac and Linux
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.
LSK-only Nanopore reads able to produce 23 gapless chromosomes , 10 scaffolded, and N50>130Mb
Huge strides have been made in assembly. Nanopore-only T2T assembly is now feasible and will soon be routine.
Many ways of answering the question “what is the genotype of my sample?”
Base calling obeys scaling laws in deep learning - a Q28 base caller using standard chemistry is now available on demand.
Base calling accuracy is compute-limited. As GPUs get faster so does accuracy!
Dorado v1.0.0 introduces dramatic improvement to modified base calling speed
Big improvements in modification calling accuracy - 6mA increases from Q16 to Q24
New HAC models are 1.4Q more accurate - a 25% error reduction
Dorado is no longer “just” a base caller - now includes alignment, mod base calling, alignment, and now even variant calling
