Hasindu Gamaarachchi
@hasindu2008.bsky.social
Lecturer at UNSW Sydney; Visiting Scientist at Garvan Institute of Medical Research -
Designing embedded systems for bioinformatics applications.
Designing embedded systems for bioinformatics applications.
Benchmark comparing SLOW5 and POD5 for nanopore raw signal data has now been published at
@GigaScience
academic.oup.com/gigascience/....
Some plots required a log scale - RAM usage and random access time.
@GigaScience
academic.oup.com/gigascience/....
Some plots required a log scale - RAM usage and random access time.
October 16, 2025 at 10:17 PM
Benchmark comparing SLOW5 and POD5 for nanopore raw signal data has now been published at
@GigaScience
academic.oup.com/gigascience/....
Some plots required a log scale - RAM usage and random access time.
@GigaScience
academic.oup.com/gigascience/....
Some plots required a log scale - RAM usage and random access time.
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:
gentechgp.github.io/gtgseq/docs/...
Reads lengths: 9.0 kbases median, 17.2 kbases mean
See:
gentechgp.github.io/gtgseq/docs/...
ONT R10.4.1 5kHz chemistry - DNA data
Open Data from Genomic Technologies Group
gentechgp.github.io
October 8, 2025 at 11:17 AM
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:
gentechgp.github.io/gtgseq/docs/...
Reads lengths: 9.0 kbases median, 17.2 kbases mean
See:
gentechgp.github.io/gtgseq/docs/...
f5c v1.6 released. Now it supports a wide range of AMD GPUs. Something me and @bonson-wong.bsky.social worked on during a hackothon organised by CSC and @pawseycentre.bsky.social
github.com/hasindu2008/...
If you have any AMD GPUs lying around, help us test the binaries.
github.com/hasindu2008/...
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.com
October 4, 2025 at 4:24 AM
f5c v1.6 released. Now it supports a wide range of AMD GPUs. Something me and @bonson-wong.bsky.social worked on during a hackothon organised by CSC and @pawseycentre.bsky.social
github.com/hasindu2008/...
If you have any AMD GPUs lying around, help us test the binaries.
github.com/hasindu2008/...
If you have any AMD GPUs lying around, help us test the binaries.
Cornetto v0.2.0-beta released
github.com/hasindu2008/...
Cornetto is not only an iterative assembly method for @nanoporetech.com, but also features some basic assembly evaluation tools that we implemented.
Suggestions and feedback welcome!
github.com/hasindu2008/...
Cornetto is not only an iterative assembly method for @nanoporetech.com, 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.com
September 13, 2025 at 11:08 PM
Cornetto v0.2.0-beta released
github.com/hasindu2008/...
Cornetto is not only an iterative assembly method for @nanoporetech.com, but also features some basic assembly evaluation tools that we implemented.
Suggestions and feedback welcome!
github.com/hasindu2008/...
Cornetto is not only an iterative assembly method for @nanoporetech.com, but also features some basic assembly evaluation tools that we implemented.
Suggestions and feedback welcome!
Reposted by Hasindu Gamaarachchi
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 @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
September 7, 2025 at 11:35 PM
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 @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
☺️
Dr Hasindu Gamaarachchi @hasindu2008.bsky.social @unsw.edu.au @garvaninstitute.bsky.social is a finalist in the Macquarie University Eureka Prize for Outstanding Early Career Researcher.
Learn more: youtu.be/FL8ZKUmtYbM
#EurekaPrizes
Learn more: youtu.be/FL8ZKUmtYbM
#EurekaPrizes
August 3, 2025 at 9:04 AM
☺️
Minimod preprint by @sunethsa.bsky.social is out
biorxiv.org/content/10.1...
-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/min...
biorxiv.org/content/10.1...
-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/min...
July 23, 2025 at 9:27 AM
Minimod preprint by @sunethsa.bsky.social is out
biorxiv.org/content/10.1...
-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/min...
biorxiv.org/content/10.1...
-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/min...
If you are at #ISMB2025:
@bosc.bsky.social track around 2:30pm ish after
@sunethsa.bsky.social's talk, Bonson Wong will present on
nanopore basecalling on AMD GPUs using slorado
github.com/BonsonW/slor...
@bosc.bsky.social track around 2:30pm ish after
@sunethsa.bsky.social's talk, Bonson Wong will present on
nanopore basecalling on AMD GPUs using slorado
github.com/BonsonW/slor...
GitHub - BonsonW/slorado: A simplified version of Dorado built on top of S/BLOW5 format.
A simplified version of Dorado built on top of S/BLOW5 format. - BonsonW/slorado
github.com
July 21, 2025 at 9:03 AM
If you are at #ISMB2025:
@bosc.bsky.social track around 2:30pm ish after
@sunethsa.bsky.social's talk, Bonson Wong will present on
nanopore basecalling on AMD GPUs using slorado
github.com/BonsonW/slor...
@bosc.bsky.social track around 2:30pm ish after
@sunethsa.bsky.social's talk, Bonson Wong will present on
nanopore basecalling on AMD GPUs using slorado
github.com/BonsonW/slor...
If you are at #ISMB2025: Go to the
@bosc.bsky.social around 2:30pm ish where
@sunethsa.bsky.social will present real-time @nanoporetech.com frequency calculation using realfreq & standalone frequency calculation using minimod.
academic.oup.com/bioinformati...
@bosc.bsky.social around 2:30pm ish where
@sunethsa.bsky.social will present real-time @nanoporetech.com frequency calculation using realfreq & standalone frequency calculation using minimod.
academic.oup.com/bioinformati...
Realfreq: real-time base modification analysis for nanopore sequencing
AbstractSummary. Nanopore sequencers allow sequencing data to be accessed in real-time. This allows live analysis to be performed, while the sequencing is
academic.oup.com
July 21, 2025 at 8:58 AM
If you are at #ISMB2025: Go to the
@bosc.bsky.social around 2:30pm ish where
@sunethsa.bsky.social will present real-time @nanoporetech.com frequency calculation using realfreq & standalone frequency calculation using minimod.
academic.oup.com/bioinformati...
@bosc.bsky.social around 2:30pm ish where
@sunethsa.bsky.social will present real-time @nanoporetech.com frequency calculation using realfreq & standalone frequency calculation using minimod.
academic.oup.com/bioinformati...
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/min...
written by
@sunethsa.bsky.social
in C, based on mod tag parsing we did for realfreq doi.org/10.1093/bioi...
github.com/warp9seq/min...
written by
@sunethsa.bsky.social
in C, based on mod tag parsing we did for realfreq doi.org/10.1093/bioi...
GitHub - warp9seq/minimod: A bioinformatics tool for viewing and calculating base modification frequencies from BAM files
A bioinformatics tool for viewing and calculating base modification frequencies from BAM files - warp9seq/minimod
github.com
July 16, 2025 at 6:16 AM
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/min...
written by
@sunethsa.bsky.social
in C, based on mod tag parsing we did for realfreq doi.org/10.1093/bioi...
github.com/warp9seq/min...
written by
@sunethsa.bsky.social
in C, based on mod tag parsing we did for realfreq doi.org/10.1093/bioi...
Reposted by Hasindu Gamaarachchi
The truly open solution is the technicallu better one here (SLOW5). Even if it was not, there would be strong reasons to prefer it. I hope the community rejects closed or strangely licensed basic tools, not just POD5, but also pseudo-open offerings like CellRanger. Good alternatives exist!
The enduring advantages of the SLOW5 file format for raw nanopore sequencing data https://www.biorxiv.org/content/10.1101/2025.06.30.662478v1
July 4, 2025 at 9:08 PM
The truly open solution is the technicallu better one here (SLOW5). Even if it was not, there would be strong reasons to prefer it. I hope the community rejects closed or strangely licensed basic tools, not just POD5, but also pseudo-open offerings like CellRanger. Good alternatives exist!
Reposted by Hasindu Gamaarachchi
blue-crab v0.4.0 has been released
- yet another end_reason added to support pod5 updates.
To convert POD5<=>S/BLOW5 it's as simple as
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...
- yet another end_reason added to support pod5 updates.
To convert POD5<=>S/BLOW5 it's as simple as
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...
Release blue-crab v0.4.0 · Psy-Fer/blue-crab
What's Changed
New paused end reason and test updates
Full Changelog: v0.3.0...v0.4.0
github.com
July 10, 2025 at 5:57 AM
blue-crab v0.4.0 has been released
- yet another end_reason added to support pod5 updates.
To convert POD5<=>S/BLOW5 it's as simple as
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...
- yet another end_reason added to support pod5 updates.
To convert POD5<=>S/BLOW5 it's as simple as
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...
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/10.1...
Summary: performance of BLOW5 is >= POD5 (from ~= to 100X, see below), with benefit of having ~3 dependencies instead of >50.
biorxiv.org/content/10.1...
Summary: performance of BLOW5 is >= POD5 (from ~= to 100X, see below), with benefit of having ~3 dependencies instead of >50.
July 5, 2025 at 4:26 AM
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/10.1...
Summary: performance of BLOW5 is >= POD5 (from ~= to 100X, see below), with benefit of having ~3 dependencies instead of >50.
biorxiv.org/content/10.1...
Summary: performance of BLOW5 is >= POD5 (from ~= to 100X, see below), with benefit of having ~3 dependencies instead of >50.
Our ex-zd compression paper is now published in Genome Research. ex-zd lossy compression mode can reduce 30-40% of the @nanopore signal data size, and the accuracy scatter is at a similar level to running the original data on two different GPUs.
genome.cshlp.org/content/35/7...
genome.cshlp.org/content/35/7...
July 2, 2025 at 12:14 AM
Our ex-zd compression paper is now published in Genome Research. ex-zd lossy compression mode can reduce 30-40% of the @nanopore signal data size, and the accuracy scatter is at a similar level to running the original data on two different GPUs.
genome.cshlp.org/content/35/7...
genome.cshlp.org/content/35/7...
Reposted by Hasindu Gamaarachchi
Ira Deveson discusses how they are using Oxford Nanopore sequencing as a single technology to provide genome assemblies to detect complex genomic regions, providing insights into underrepresented populations, rare disease and more. #NanoporeConf
May 22, 2025 at 12:44 PM
Ira Deveson discusses how they are using Oxford Nanopore sequencing as a single technology to provide genome assemblies to detect complex genomic regions, providing insights into underrepresented populations, rare disease and more. #NanoporeConf
Reposted by Hasindu Gamaarachchi
New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention).
www.biorxiv.org/content/10.1...
(1/6)
www.biorxiv.org/content/10.1...
(1/6)
Autocycler: long-read consensus assembly for bacterial genomes
Motivation Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using T...
www.biorxiv.org
May 21, 2025 at 3:29 AM
New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention).
www.biorxiv.org/content/10.1...
(1/6)
www.biorxiv.org/content/10.1...
(1/6)
Attending my first inperson London calling #nanoporeconf
May 21, 2025 at 12:58 PM
Attending my first inperson London calling #nanoporeconf
Reposted by Hasindu Gamaarachchi
New postdoc opening @ UNSW in RNA biology and T cell immunity 🥼🧬🧫. Use molecular biology, nanopore sequencing, and in vivo models to uncover the regulatory drivers of adaptive immunity. Apply 👉 external-careers.jobs.unsw.edu.au/cw/en/job/53...
Postdoctoral Fellow/Senior Research Associate
UNSW is seeking an enthusiastic researcher for an exciting new role involving dynamic collaboration within a multidisciplinary team of immunologists, RNA biologists and bioinformaticians. Sponsorship ...
external-careers.jobs.unsw.edu.au
May 13, 2025 at 10:46 PM
New postdoc opening @ UNSW in RNA biology and T cell immunity 🥼🧬🧫. Use molecular biology, nanopore sequencing, and in vivo models to uncover the regulatory drivers of adaptive immunity. Apply 👉 external-careers.jobs.unsw.edu.au/cw/en/job/53...
Reposted by Hasindu Gamaarachchi
We are scheduling two exciting SAFARI-EFCL joint seminar talks on accelerating genome analysis!
On May 27th at 10 AM (CEST), @hasindu2008.bsky.social will give a talk on "Scalable, Efficient and Real-time Analysis of Long-read Genomic Data"
More on this talk: safari.ethz.ch/safari-efcl-... (1/3)
On May 27th at 10 AM (CEST), @hasindu2008.bsky.social will give a talk on "Scalable, Efficient and Real-time Analysis of Long-read Genomic Data"
More on this talk: safari.ethz.ch/safari-efcl-... (1/3)
SAFARI-EFCL Joint Seminar: Hasindu Gamaarachchi, May 27 2025 – SAFARI Research Group
safari.ethz.ch
May 12, 2025 at 4:12 PM
We are scheduling two exciting SAFARI-EFCL joint seminar talks on accelerating genome analysis!
On May 27th at 10 AM (CEST), @hasindu2008.bsky.social will give a talk on "Scalable, Efficient and Real-time Analysis of Long-read Genomic Data"
More on this talk: safari.ethz.ch/safari-efcl-... (1/3)
On May 27th at 10 AM (CEST), @hasindu2008.bsky.social will give a talk on "Scalable, Efficient and Real-time Analysis of Long-read Genomic Data"
More on this talk: safari.ethz.ch/safari-efcl-... (1/3)
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
@nanoporetech.com MinION sequencer, and a desktop a PromethION 2 solo flowcell.
academic.oup.com/bioinformati...
Written efficiently using C, a laptop can keep up with a
@nanoporetech.com MinION sequencer, and a desktop a PromethION 2 solo flowcell.
academic.oup.com/bioinformati...
Realfreq: real-time base modification analysis for nanopore sequencing
AbstractSummary. Nanopore sequencers allow sequencing data to be accessed in real-time. This allows live analysis to be performed, while the sequencing is
academic.oup.com
May 3, 2025 at 4:45 AM
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
@nanoporetech.com MinION sequencer, and a desktop a PromethION 2 solo flowcell.
academic.oup.com/bioinformati...
Written efficiently using C, a laptop can keep up with a
@nanoporetech.com MinION sequencer, and a desktop a PromethION 2 solo flowcell.
academic.oup.com/bioinformati...
This new Hifiasm --ont option is amazing. It worked like a charm for us in the nanopore adaptive sampling based assembly paradigm we introduced in a preprint recently.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
April 19, 2025 at 2:31 AM
This new Hifiasm --ont option is amazing. It worked like a charm for us in the nanopore adaptive sampling based assembly paradigm we introduced in a preprint recently.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Introducing cornetto, an adaptive genome assembly paradigm using @nanoporetech.com 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.
- 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.
Adaptively integrated sequencing and assembly of near-complete genomes https://www.biorxiv.org/content/10.1101/2025.03.31.646505v1
April 5, 2025 at 4:07 AM
Introducing cornetto, an adaptive genome assembly paradigm using @nanoporetech.com 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.
- 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.
Reposted by Hasindu Gamaarachchi
Uncalled4: a toolkit for nanopore signal alignment, analysis and visualization of DNA and RNA modifications.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
March 28, 2025 at 5:23 PM
Uncalled4: a toolkit for nanopore signal alignment, analysis and visualization of DNA and RNA modifications.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Slorado v0.3.0 released with support for v5 transformer models.
github.com/BonsonW/slorado
anyone with a @nanoporetech.com 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-bas...
github.com/BonsonW/slorado
anyone with a @nanoporetech.com 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-bas...
March 29, 2025 at 11:46 PM
Slorado v0.3.0 released with support for v5 transformer models.
github.com/BonsonW/slorado
anyone with a @nanoporetech.com 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-bas...
github.com/BonsonW/slorado
anyone with a @nanoporetech.com 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-bas...
For those who want to run nanopore basecalling on the Australia'a @pawseycentre.bsky.social supercomputer (or any other AMD GPU clusters in general):
pawsey.org.au/pawsey-enabl...
pawsey.org.au/pawsey-enabl...
Pawsey enables more flexible and scalable DNA analysis - Pawsey Supercomputing Research Centre
Researchers use Pawsey's Setonix supercomputer to develop Slorado, the first open-source software for nanopore sequencing on AMD GPUs, expanding bioinformatics capabilities worldwide. Register for the...
pawsey.org.au
February 26, 2025 at 11:11 PM
For those who want to run nanopore basecalling on the Australia'a @pawseycentre.bsky.social supercomputer (or any other AMD GPU clusters in general):
pawsey.org.au/pawsey-enabl...
pawsey.org.au/pawsey-enabl...