Hiruna Samarakoon

We wrote Slow5tools to complement SLOW5 format. It runs fast, does all kinds of file processing tasks, and compiles with the minimum dependencies. Give our preprint a read.

I've drafted some personal suggestions for improving the usability of bioinformatic (command-line) tools, hoping all tools will be easy to install and use.😀 Pull requests are welcome. github.com/shenwei356/per…

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).

For many of those who were asking on BLOW5 vs POD5 for nanopore signal data, here is a finally detailed benchmark we did: biorxiv.org/content/10.110… Summary: performance of BLOW5 is >= POD5 (from ~= to 100X, see below), with benefit of having ~3 dependencies instead of >50.

Congratulations to Hasindu Gamaarachchi who has been awarded the 2024 ‘Torsten Seemann’ Outstanding Bioinformatics Software Developer Award from the ABACBS. This award recognises an outstanding early/mid-career bioinformatics software developer from the Australian community.

We are hosting a Long Read Research Symposium at @GarvanInstitute ! Our talented speakers will cover the advantages of both @nanopore and @PacBio data. Join us to find out what long reads could do for you 🧬 eventbrite.com.au/e/garvan-long-…

As a few of you requested at #ISMB2024, here is an entry-level tutorial to get started with nanopore signal data with SLOW5 hasindu2008.github.io/slow5/tutorial written by @mungbungo

Squigulator, our simple tool for simulating nanopore raw signal data, is now published in @genomeresearch. See genome.cshlp.org/content/34/5/7… Quite a few useful RNA-related features suggested by the reviewers are in the latest release: github.com/hasindu2008/sq…

slow5lib v1.2.0 (and pyslow5) + slow5tools v.1.20 released github.com/hasindu2008/sl… github.com/hasindu2008/sl… - big-endian architecture support - documentation added for the easy multithread API - more documentation and usability improvements

New work from @hasindu2008 et al. expanding the SLOW5 ecosystem to improve remote access to @nanopore signal datasets. Streamlining remote nanopore data access with slow5curl doi.org/10.1093/gigasc…

Really can't stand the heat. It's really really hot, and too hot to do any work. Physical or desk work. Can't we have an accelerated plan to plant as many trees as possible everywhere in Sri Lanka? It's always cooler where there are more trees. #ClimateCrisis #GlobalWarming

We have released some raw @nanopore data for benchmarking purposes, along with some basecalled outputs. We use the subset of 20k or 500k for benchmarking tools and methods a LOT! We thought they would be helpful to others too. 4/5kHz R10.4.1 & RNA004 gentechgp.github.io/gtgseq/

Our #slow5curl paper is out! academic.oup.com/gigascience/ar… Big projects storing hundreds/thousands of @nanopore signal datasets on cloud storage like @awscloud #s3 will be able to save 💸,⏲️ and bandwidth while improving the accessibility of datasets to those with limited computing ..

slow5curl, a software package designed to streamline nanopore data sharing, accessibility, and reanalysis. academic.oup.com/gigascience/ar…

See the preprint for squigualiser for visualising @nanopore signal pileups for RNA/DNA. Supports alignments from multiple signal tool/aligners such as f5c, guppy/dorado moves, squigulator etc.

Take a break from worrying about the AllOfUs Umap and check out Squigualiser- our new tool for @nanopore signal data exploration. Great engineering by @hiruna72 and @Hasindu2008 as always 🔥🔥biorxiv.org/content/10.110…