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…

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 Suneth in C, based on mod tag parsing we did for realfreq doi.org/10.1093/bioinf…

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 Oxford Nanopore r10 and r9 dna signal-to-reference comparison (check Advanced Examples in repo).

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

If you are at #ISMB2025: #BOSC2025 track around 2:30pm ish after Suneth's talk , bonson wong will present on Oxford Nanopore basecalling on AMD GPUs using slorado [github.com/BonsonW/slorado]

Minimod preprint by Suneth 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…

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

Longdust, a new tool to identify highly repetitive STRs, VNTRs, satellite DNA and other low-complexity regions (LCRs). Similar to SDUST but for long regions. github.com/lh3/longdust

Come join us this November 13th for the Garvan Long-Read Research Symposium! You'll hear about the wonderful things you can do with Oxford Nanopore and PacBio long reads from a great line-up of speakers. FREE to attend. Register below eventbrite.com.au/e/garvan-long-…

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 and supervised by Heng Li Heng Li

minimap2.com is potentially a phishing site. Please don't use anything from that website. github.com/lh3/minimap2/i…

Cornetto v0.2.0-beta released github.com/hasindu2008/co… Cornetto is not only an iterative assembly method for Oxford Nanopore, but also features some basic assembly evaluation tools that we implemented. Suggestions and feedback welcome!

f5c v1.6 released. Now it supports a wide range of AMD GPUs. Something me and bonson wong worked on during a hackothon organised by CSC and Pawsey Supercomputing Research Centre github.com/hasindu2008/f5… If you have any AMD GPUs lying around, help us test the binaries.

For anyone interested, we uploaded another new HG002 Oxford 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/da…

Blow5 is the archival format of choice for all internal ONT raw data around here. IMHO slow5 output also makes it easy to look at the raw signal data and play around with it for learning & analysis purposes. I should really write up some visualization tutorials soon.