Hasindu Gamaarachchi

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/minim… written by @sunethsam in C, based on mod tag parsing we did for realfreq doi.org/10.1093/bioinf…

Minimod preprint by @sunethsam is out biorxiv.org/content/10.110… -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/minim…

If you are at #ISMB2025: #BOSC2025 track around 2:30pm ish after @sunethsam's talk , @bonson_wong will present on @nanopore basecalling on @AMD GPUs using slorado [github.com/BonsonW/slorado]

If you are at #ISMB2025: Go to the #BOSC2025 track around 2:30pm ish where @sunethsam will present on real-time @nanopore realtime modification frequency calculation using realfreq [academic.oup.com/bioinformatics…] and standalone frequency calculation using minimod.

New squigualiser-v0.6.4 is out with a new subtool to plot signals (plot_signal) 🚀Just download and execute our standalone binaries (linux/macos). github.com/hiruna72/squig… Below is @nanopore r10 and r9 dna signal-to-reference comparison (check Advanced Examples in repo).

blue-crab v0.4.0 released - yet another end_reason added to support pod5 updates. To convert POD5<=>S/BLOW5 simply: 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-c…

Our ex-zd compression is now published in Genome Research. ex-zd lossy mode can reduce 30-40% of the @nanopore signal data size, and the basecalling accuracy scatter is at a similar level to running the original data on two different GPUs - V100 vs A100. genome.cshlp.org/content/35/7/1…

Join us next week for two joint SAFARI-EFCL Seminars! @Hasindu2008 will present "Scalable, Efficient and Real-time Analysis of Long-read Genomic Data", at 10AM in CAB G61 and online: Livestream Tuesday, May 27, 10AM CEST: youtube.com/live/MUbk7PCUO… @FirtinaC @_onurmutlu_

Attending my first in person London calling #Nanoporeconf

Just casually doing some SUP basecalling on an AMD 7900XTX GPU 😅 with ROCm in a workstation at home. A work in progress by Hasindu and Bonson in the lab.

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 @nanopore MinION sequencer, and a desktop a PromethION 2 solo flowcell. academic.oup.com/bioinformatics…

New preprint on hifiasm (ONT)! We can now achieve near T2T human genome assembly using only ONT Simplex reads—in just half a day, with or without ultra-long sequencing. biorxiv.org/content/10.110…

Congrats @Hasindu2008 and Nanopore Garvan team. This is an exciting development. I remember asking myself how AS might be used when it was first released. You have truely answered this 🙌🎉

Introducing cornetto, an adaptive genome assembly paradigm using @nanopore 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.

Computational analysis of DNA methylation from long-read sequencing nature.com/articles/s4157…

Uncalled4: a toolkit for nanopore signal alignment, analysis and visualization of DNA and RNA modifications. nature.com/articles/s4159…

Slorado v0.3.0 released with support for v5 transformer models. github.com/BonsonW/slorado anyone with a @nanopore 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-basec…