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Hasindu Gamaarachchi @hasindu2008.bsky.social · 01/06/2026

Are you planning to switch to rust from C for future programs?

Hasindu Gamaarachchi @hasindu2008.bsky.social · 07/05/2026

Yeh, that ARM emulation on x86 was like a sloth, but I think now there is native ones on Git actions. That action for BSD seems nice! I may adapt this 😀

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 05/05/2026

Then it should ARM. Modkit cannot be compiled for ARM?

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 05/05/2026

Is it cpu software or gpu software?

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 30/04/2026

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...

github.com

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...

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 26/04/2026

Perhaps, in a github standard runner, use the container option and can specify a freebsd image? Kind of emulation though. I have been using this way to test on older distributions with old gcc, like ubuntu20 and has been working ok. github.com/hasindu2008/...

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 28/03/2026

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

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Reposted by Hasindu Gamaarachchi

Jim Shaw @jimshaw.bsky.social · 27/03/2026

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

rdcu.be

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.

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 24/03/2026

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

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Reposted by Hasindu Gamaarachchi

Eduardo Eyras @edueyras.bsky.social · 28/01/2026

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

biorxiv.org

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 28/01/2026

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...

github.com

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...

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 22/01/2026

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 [github.com/hasindu2008/nci-scripts] to demonstrate how these can be used.

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 06/12/2025

Yes that is the process. Very detailed step are here: hasindu2008.github.io/cornetto/doc... If you run into obstacles when setup, please open an issue - will be helful for us to streamline the setup steps where possible.

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 06/12/2025

Yes, it works with MinION. I have detailed the steps here: hasindu2008.github.io/cornetto/doc... Not sure if this is simple enough though :D

hasindu2008.github.io

Cornetto bioinformatics protocol

adaptive genome assembly using nanopore sequencing

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Reposted by Hasindu Gamaarachchi

Mihail Zdravkov @mzdravkov.mastodon.green.ap.brid.gy · 05/12/2025

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: codeberg.org/mzdravkov/Slow5.jl

codeberg.org

Slow5.jl

A Julia wrapper for slow5lib

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 04/12/2025

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’.

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 26/11/2025

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

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 26/11/2025

Cornetto uses readfish by @minomatt.bsky.social for adaptive sampling & hifiasm by Hayou, @lh3lh3.bsky.social et al for assembly.

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 26/11/2025

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...

amd.com

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 30/10/2025

possibly because ONT use their POD5 format which is not great on HDD. They could have adopted our slow5 format which we showed long ago that works for even HDD, before pod5 came in. Now the pod5 (while indeed better than fast5) is still behind slow5 in this regards academic.oup.com/gigascience/...

academic.oup.com

The enduring advantages of the SLOW5 file format for raw nanopore sequencing data

Abstract. Nanopore sequencing is a widespread and important method in genomics science. The raw electrical current signal data from a typical nanopore sequ

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 30/10/2025

Sometime ago I changed a configuration file so this location is changed to our /data location permanently. Don't know if they have changed this option now.

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 21/10/2025

Yeh, many better ways exist. We just showed how the most naive method can still keep up truck load volumes of data.

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 21/10/2025

In my personal opinion, more popular it is, more care should be taken to avoid compatibility problems. Adhoc implementation-driven changes can be avoided if enough thought is given at the design phase.

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 21/10/2025

Just checked my logs and yes it is true. The output produced was wrong - A simple program that sums up the signal values. I just checked release logs of pod5 - 0.0.20 "Fix bug reading data via C API". So it could be a bug that got introduced in before.

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 16/10/2025

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.

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 08/10/2025

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/...

gentechgp.github.io

ONT R10.4.1 5kHz chemistry - DNA data

Open Data from Genomic Technologies Group

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 14/09/2025

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.com

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

adaptive genome assembly using nanopore sequencing - hasindu2008/cornetto

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 12/09/2025

Meanwhile, questions by me and @psy-fer.bsky.social on POD5 writing opened months ago are yet to be answered by ONT. It is very interesting that they have skipped those questions 🤣

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 12/09/2025

Any possibility of getting something akin to the "lowQ.bed" that hifiasm output indicating the low-quality regions in the assembly?

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 11/09/2025

Nice! We plan to try this out with adaptive sampling for metagenomes, like we did in cornetto with hifiasm [doi.org/10.1101/2025.03.31.646505] for genome assemblies.

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Reposted by Hasindu Gamaarachchi

Jim Shaw @jimshaw.bsky.social · 08/09/2025

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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Hasindu Gamaarachchi @hasindu2008.bsky.social · 09/09/2025

seriously? I am glad that some time ago, I disabled this Gemini summary from my search results when it was pushed out. Seems I should better keep it that way😂

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 23/07/2025

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...

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 21/07/2025

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.com

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

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 18/07/2025

For reference based frequency finding, thought taking the bases that only match the ref could be a better choice. But yes, such a warning is indeed something that would be valuable. Thank you very much for the suggestion

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 18/07/2025

I get these then, 6754 6751 6769 6760 6756 Which seem to match the expected, assuming you are using 1-based coordinates

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