Hasindu Gamaarachchi

@Hasindu2008

Lecturer at UNSW Sydney; Visiting Scientist at Garvan Institute of Medical Research - Designing embedded systems for bioinformatics applications.

Sydney, New South Wales

linkedin.com/in/hasindugama…

Joined May 2012

788 Following

1,276 Followers

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Hasindu Gamaarachchi
@Hasindu2008
Apr 30
We have released slorado v0.5.0-beta and now it supports Nanopore DNA methylation calling (5mCG_5hmCG). Also 20% performance improvement to SUP models. Slorado supports both NVIDIA and AMD GPUs. github.com/BonsonW/slorad… @bonson_wong @GaganGdas
Release slorado-v0.5.0-beta · BonsonW/slorado
From github.com
Hasindu Gamaarachchi
@Hasindu2008
Mar 28
The pre-print for Slorado and openfish is out. biorxiv.org/content/10.648… You can do @nanopore basecalling with not just NVIDIA GPU, but also using a range of AMD GPU. Would be useful since popular GPUs are now 💸💸💸💸(& hard to buy), Work by @bonson_wong
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Hasindu Gamaarachchi
@Hasindu2008
Mar 24
We have released minimod v0.5.0. Now support a number of different modifications other than CpG methylation.
Suneth
@sunethsam
Mar 24
We've just released Minimod v0.5.0! 🧬 Minimod is a fast, lightweight tool for extracting modifications and computing frequencies from aligned BAM files (with MM/ML tags). Check it out github.com/warp9seq/minim… #Bioinformatics #Genomics #Epigenetics #ONT #PacBio #OpenSource
Hasindu Gamaarachchi
@Hasindu2008
Jan 28
slow5tools v1.4.0 released Many bit profiles for ex-zd lossy compression added by @hiruna72, who reduced 275TB of historical @nanopore rawdata at @GenTechGp to 172TB. guide to lossy archive: hasindu2008.github.io/slow5tools/arc… paper: doi.org/10.1101/gr.280… release: github.com/hasindu2008/sl…
hasindu2008.github.io
A Guide for Archiving Lossy Data
Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.
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Hasindu Gamaarachchi
@Hasindu2008
Jan 22
Now that the @NCInews Gadi supercomputer in Australia has H200 GPUs, @nanopore super-accuracy basecalling+modcalling is much faster than before. For those who are interested, I have updated my example scripts [github.com/hasindu2008/nc…] to demonstrate how these can be used.
GitHub - hasindu2008/nci-scripts: PBS scripts for running nanopore genomics analyses on NCI Gadi
From github.com
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