RT @GenTechGp: Come join us this November 13th for the Garvan Long-Read Research Symposium! You'll hear about the wonderful things you can….

RT @eurekaprizes: Dr Hasindu Gamaarachchi @Hasindu2008 @unsw is a finalist in the @Macquarie_Uni Eureka Prize for Outstanding Early Career….

RT @lh3lh3: Longdust, a new tool to identify highly repetitive STRs, VNTRs, satellite DNA and other low-complexity regions (LCRs). Similar….

Minimod preprint by @sunethsam is out .-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:

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 [.

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 [ and standalone frequency calculation using minimod.

RT @hiruna72: New squigualiser-v0.6.4 is out with a new subtool to plot signals (plot_signal) 🚀Just download and execute our standalone bin….

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. written by @sunethsam in C, based on mod tag parsing we did for realfreq

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

This shows the technicality (previously known) that using mmap for reading large files with predictable access pattern which the programmer can well know in advance than what the operating system can guess -> can lead to unpredicable performance outcomes.

Key observations.- sequential access: BLOW5 ~7X faster on academic HPC we tested. Similar performance on desktops with single SSD drives. - random access: BLOW5 is always significantly fast (sometimes 100X).- size: similar if same compression.- Dependencies: BLOW5 ~3, POD5 >50.

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

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.

RT @SAFARI_ETH_CMU: Join us next week for two joint SAFARI-EFCL Seminars! @Hasindu2008 will present "Scalable, Efficient and Real-time Ana….

Attending my first in person London calling #Nanoporeconf

RT @Psy_Fer_: Just casually doing some SUP basecalling on an AMD 7900XTX GPU 😅 with ROCm in a workstation at home. A work in progress by H….

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.

RT @ChengChhy: New preprint on hifiasm (ONT)! We can now achieve near T2T human genome assembly using only ONT Simplex reads—in just half a….

RT @bach_warren: Congrats @Hasindu2008 and Nanopore Garvan team. This is an exciting development. I remember asking myself how AS might be….

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.