We have released slorado v0.5.0-beta and now it supports Nanopore DNA methylation calling (5mCG_5hmCG). Also 20% performance improvement to SUP models. Slorado supports both NVIDIA and AMD GPUs. github.com/BonsonW/slor...

Release slorado-v0.5.0-beta · BonsonW/slorado

What's Changed Experimental methylation detection support by specifying the --mod 5mCG_5hmCG@v3 option. Works with HAC and SUP v5.0.0 DNA GPU basecalling models Transformer (SUP >= v5.0.0) model o...

github.com

The pre-print for Slorado and openfish is out. biorxiv.org/content/10.6... You can do @nanoporetech.com basecalling with not just NVIDIA GPU, but also using a range of AMD GPU. Would be useful since popular GPUs are now 💸💸💸💸(& hard to buy), Work by @bonson-wong.bsky.social

Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback. rdcu.be/famFj

High-resolution metagenome assembly for modern long reads with myloasm

Nature Biotechnology - A long-read metagenome assembly method recovers circular and complete genomes better than existing tools.

rdcu.be

Nature Biotechnology@natbiotech.nature.com · 4mo ago

High-resolution metagenome assembly for modern long reads with myloasm - @lh3lh3.bsky.social @jimshaw.bsky.social @danafarber.bsky.social @harvardmed.bsky.social go.nature.com/3PBEwvR

We have released minimod v0.5.0. Now supports a number of different modifications other than CpG methylation.

@sunethsa.bsky.social · 4mo ago

We've just released Minimod v0.5.0! 🧬 Minimod is a fast, lightweight tool for extracting modifications and computing frequencies from aligned BAM files (with MM/ML tags). Check it out github.com/warp9seq/min... #Bioinformatics #Genomics #Epigenetics #ONT #PacBio #OpenSource

Excited to share our latest preprint: "SWARM: A Single-Molecule Workflow for High-Precision Profiling of RNA Modifications" www.biorxiv.org/content/10.6... Led by Stefan Prodic #RNA #Epitranscriptomics #Nanopore 1/6

slow5tools v1.4.0 released github.com/hasindu2008/... Many bit profiles for ex-zd lossy compression added by @hiruna72, who reduced 275TB of historical @nanopore rawdata at @GenTechGp to 172TB. guide to lossy archive: hasindu2008.github.io/slow5tools/a... paper: doi.org/10.1101/gr.2...

Release slow5tools-v1.4.0 · hasindu2008/slow5tools

What's Changed slow5tools skim supports the new auxiliary field open_pore_level introduced in latest ONT pod5 slow5tools degrade has new profiles added (by @sashajenner and @hiruna72) and are docu...

github.com

Now that the @nci-australia.bsky.social Gadi supercomputer in Australia has H200 GPUs, @nanopore basecalling is much faster than before. For those who are interested, I have updated my example scripts [https://github.com/hasindu2008/nci-scripts] to demonstrate how these can be used.

slorado v0.4.0-beta is released: github.com/BonsonW/slor... - Support for RNA basecalling - 20-35% performance improvement for super-accuracy basecalling Work by @bonson-wong.bsky.social.

Release slorado-v0.4.0-beta · BonsonW/slorado

What's Changed Support for RNA models >= v5.1.0 --flash yes|no option that enables flash attention for transformer models (SUP >= v5.0.0). This is "no" by default to maximise compatibility across ...

github.com

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’.

Hasindu Gamaarachchi@hasindu2008.bsky.social · 8mo ago

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.

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.

Targeted sequencing and iterative assembly of near-complete genomes - Nature Communications

Long-read sequencing enables high-quality genome assemblies, but challenges remain. Here, the authors introduce Cornetto, a method that improves assembly quality, enables genome sequencing from saliva...

nature.com

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.

Release f5c-v1.6 · hasindu2008/f5c

What's Changed updated slow5lib to 1.3 to support ex-zd compressed blow5 fix unnecessary tab being printed in resquiggle tsv output [see #180 ] improvements to error/warning messages f5c now suppo...

github.com

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!

GitHub - hasindu2008/cornetto: adaptive genome assembly using nanopore sequencing

adaptive genome assembly using nanopore sequencing - hasindu2008/cornetto

github.com

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

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 11mo ago

High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1

☺️

Australian Museum Eureka Prizes@eurekaprizes.bsky.social · last yr.

Dr Hasindu Gamaarachchi @hasindu2008.bsky.social @unsw.edu.au @garvaninstitute.bsky.social is a finalist in the Macquarie University Eureka Prize for Outstanding Early Career Researcher. Learn more: youtu.be/FL8ZKUmtYbM #EurekaPrizes

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...

GitHub - BonsonW/slorado: A simplified version of Dorado built on top of S/BLOW5 format.

A simplified version of Dorado built on top of S/BLOW5 format. - BonsonW/slorado

github.com

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...

Realfreq: real-time base modification analysis for nanopore sequencing

AbstractSummary. Nanopore sequencers allow sequencing data to be accessed in real-time. This allows live analysis to be performed, while the sequencing is

academic.oup.com

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...

GitHub - warp9seq/minimod: A bioinformatics tool for viewing and calculating base modification frequencies from BAM files

A bioinformatics tool for viewing and calculating base modification frequencies from BAM files - warp9seq/minimod

github.com

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!

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · last yr.

The enduring advantages of the SLOW5 file format for raw nanopore sequencing data https://www.biorxiv.org/content/10.1101/2025.06.30.662478v1

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...

Release blue-crab v0.4.0 · Psy-Fer/blue-crab

What's Changed New paused end reason and test updates Full Changelog: v0.3.0...v0.4.0

github.com

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)

Autocycler: long-read consensus assembly for bacterial genomes

Motivation Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using T...

biorxiv.org

Attending my first inperson London calling #nanoporeconf