Mastodawn

Also, @bonson-wong did a slow5curl release https://github.com/BonsonW/slow5curl/releases/tag/v0.3.0 to support these ex-zd compressed BLOW5

Release slow5curl-v0.3.0 · BonsonW/slow5curl

Whats Changed Can now download ex-zd compressed SLOW5/BLOW5 files Update to slow5lib-v1.4.0 Minor usability and documentation improvements Full Changelog: v0.2.1...v0.3.0

GitHub

Hasindu Gamaarachchi Jan 28

slow5tools v1.4.0 released https://github.com/hasindu2008/slow5tools/releases/tag/v1.4.0

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: https://hasindu2008.github.io/slow5tools/archive-lossy.html
paper: https://doi.org/10.1101/gr.280090.124

Hasindu Gamaarachchi Jan 22

Now that the NCI 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.

GitHub - hasindu2008/nci-scripts: PBS scripts for running nanopore genomics analyses on NCI Gadi

PBS scripts for running nanopore genomics analyses on NCI Gadi - hasindu2008/nci-scripts

GitHub

Hasindu Gamaarachchi Jan 14

slorado v0.4.0-beta is released: https://github.com/BonsonW/slorado/releases/tag/v0.4.0-beta
- Support for RNA basecalling
- 20-35% performance improvement for super-accuracy basecalling

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

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Hasindu Gamaarachchi Oct 16

@Psy_Fer_ @GigaScience

Hasindu Gamaarachchi Oct 16

Benchmark comparing SLOW5 and POD5 for nanopore raw signal data has now been published at
@GigaScience

https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giaf118/8287640?utm_source=advanceaccess&utm_campaign=gigascience&utm_medium=email.

Some plots required a log scale - RAM usage and random access time.

Hasindu Gamaarachchi Oct 8

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:
https://gentechgp.github.io/gtgseq/docs/data.html#na24385-hg002-promethion-data-40x-longer-reads-enzyme-e821

ONT R10.4.1 5kHz chemistry - DNA data

Open Data from Genomic Technologies Group

gtgseq

Hasindu Gamaarachchi Oct 4

f5c v1.6 released. Now it supports a wide range of AMD GPUs.

https://github.com/hasindu2008/f5c/releases/tag/v1.6

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

Hasindu Gamaarachchi Sep 13, 2025

Cornetto v0.2.0-beta released
https://github.com/hasindu2008/cornetto
Cornetto is not only an iterative assembly method for nanopore, 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

Hasindu Gamaarachchi Jul 23, 2025

Minimod preprint is out
https://biorxiv.org/content/10.1101/2025.07.16.665072v1
-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: https://github.com/warp9seq/minimod