I made a small wrapper library for reading slow5/blow5 files in #julialang based on the C slow5lib. If anyone working with #Nanopore sequencing is interested, you can find it here: https://codeberg.org/mzdravkov/Slow5.jl

Cornetto v0.2.0 is now released for using programmable selective nanopore sequencing for genome assembly. GitHub: github.com/hasindu2008/... Paper: nature.com/articles/s41... Datasets: hasindu2008.github.io/cornetto/doc... ... and a banner made by Ira Deveson referring to ‘no boring bits’.

Congratulations Hiruna Samarakoon (yet to be on bluesky) for winning the #abacbs2025 “Torsten Seemann” Outstanding Bioinformatics Software Developer Award!!! 🎉🎉🎉

Our cornetto work is now published at www.nature.com/articles/s41... It can do near-T2T assembly using @nanoporetech.com adaptive sampling - with less 💸 - reference agnostic, so works for non-humans - not just blood, even saliva Just presented at #abacbs2025 yesterday.

With Slorado, now you have more choices for GPUs when basecalling @nanoporetech.com sequencing data. This is a work we collaborated on with AMD, led by PhD candidate @bonson-wong.bsky.social (poster at #abacbs2025) and great to see being highlighted in the AMD blog: www.amd.com/en/blogs/202...

Benchmark comparing SLOW5 and POD5 for nanopore raw signal data has now been published at @GigaScience academic.oup.com/gigascience/.... Some plots required a log scale - RAM usage and random access time.

For anyone interested, we uploaded another new HG002 @nanopore R10.4.1 (e8.2.1 enzyme) dataset with raw signals and super-accurate basecalls. Reads lengths: 9.0 kbases median, 17.2 kbases mean See: gentechgp.github.io/gtgseq/docs/...

f5c v1.6 released. Now it supports a wide range of AMD GPUs. Something me and @bonson-wong.bsky.social worked on during a hackothon organised by CSC and @pawseycentre.bsky.social github.com/hasindu2008/... If you have any AMD GPUs lying around, help us test the binaries.

Cornetto v0.2.0-beta released github.com/hasindu2008/... Cornetto is not only an iterative assembly method for @nanoporetech.com, but also features some basic assembly evaluation tools that we implemented. Suggestions and feedback welcome!

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N

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Minimod preprint by @sunethsa.bsky.social is out biorxiv.org/content/10.1... -similar accuracy to modkit & pb-CpG-tools. -standard open-source licenses (NOT vendor-specific) -Simple but faster, on a laptop ~4X for DNA and ~55X for RNA. Code: github.com/warp9seq/min...

If you are at #ISMB2025: @bosc.bsky.social track around 2:30pm ish after @sunethsa.bsky.social's talk, Bonson Wong will present on nanopore basecalling on AMD GPUs using slorado github.com/BonsonW/slor...

If you are at #ISMB2025: Go to the @bosc.bsky.social around 2:30pm ish where @sunethsa.bsky.social will present real-time @nanoporetech.com frequency calculation using realfreq & standalone frequency calculation using minimod. academic.oup.com/bioinformati...

We've been developing a small standalone tool for viewing & calculating frequency from modification tags in BAM files. This call is for brave users to test. github.com/warp9seq/min... written by @sunethsa.bsky.social in C, based on mod tag parsing we did for realfreq doi.org/10.1093/bioi...

The truly open solution is the technicallu better one here (SLOW5). Even if it was not, there would be strong reasons to prefer it. I hope the community rejects closed or strangely licensed basic tools, not just POD5, but also pseudo-open offerings like CellRanger. Good alternatives exist!

blue-crab v0.4.0 has been released - yet another end_reason added to support pod5 updates. To convert POD5<=>S/BLOW5 it's as simple as pip install blue-crab pod5->blow5 blue-crab p2s example.pod5 -o example.blow5 blow5->pod5 blue-crab s2p example.blow5 -o example.pod5 github.com/Psy-Fer/blue...

For many of those who were asking on BLOW5 vs POD5 for nanopore signal data, here is a finally detailed benchmark we did: biorxiv.org/content/10.1... Summary: performance of BLOW5 is >= POD5 (from ~= to 100X, see below), with benefit of having ~3 dependencies instead of >50.

Our ex-zd compression paper is now published in Genome Research. ex-zd lossy compression mode can reduce 30-40% of the @nanopore signal data size, and the accuracy scatter is at a similar level to running the original data on two different GPUs. genome.cshlp.org/content/35/7...

Ira Deveson discusses how they are using Oxford Nanopore sequencing as a single technology to provide genome assemblies to detect complex genomic regions, providing insights into underrepresented populations, rare disease and more. #NanoporeConf

New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention). www.biorxiv.org/content/10.1... (1/6)

Attending my first inperson London calling #nanoporeconf

New postdoc opening @ UNSW in RNA biology and T cell immunity 🥼🧬🧫. Use molecular biology, nanopore sequencing, and in vivo models to uncover the regulatory drivers of adaptive immunity. Apply 👉 external-careers.jobs.unsw.edu.au/cw/en/job/53...

We are scheduling two exciting SAFARI-EFCL joint seminar talks on accelerating genome analysis! On May 27th at 10 AM (CEST), @hasindu2008.bsky.social will give a talk on "Scalable, Efficient and Real-time Analysis of Long-read Genomic Data" More on this talk: safari.ethz.ch/safari-efcl-... (1/3)

Realfreq, a framework for real-time base modification analysis for nanopore sequencing, is now published in Bioinformatics. Written efficiently using C, a laptop can keep up with a @nanoporetech.com MinION sequencer, and a desktop a PromethION 2 solo flowcell. academic.oup.com/bioinformati...

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...

Introducing cornetto, an adaptive genome assembly paradigm using @nanoporetech.com adaptive sampling. - greatly reduces cost per genome assembly - reference agnostic, so works for non-humans - assembly just using saliva - & many more Relies on 2 excellent software #readfish & #hifiasm.

Uncalled4: a toolkit for nanopore signal alignment, analysis and visualization of DNA and RNA modifications. www.nature.com/articles/s41...

Slorado v0.3.0 released with support for v5 transformer models. github.com/BonsonW/slorado anyone with a @nanoporetech.com dataset and AMD GPU please could give a try with binaries. Some details on how we implemented slorado in blog article pawsey.org.au/nanopore-bas...

For those who want to run nanopore basecalling on the Australia'a @pawseycentre.bsky.social supercomputer (or any other AMD GPU clusters in general): pawsey.org.au/pawsey-enabl...