Hasindu Gamaarachchi
@Hasindu2008
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Lecturer at UNSW Sydney; Visiting Scientist at Garvan Institute of Medical Research - Designing embedded systems for bioinformatics applications.
Sydney, New South Wales
Joined May 2012
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.
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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.
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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.
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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.
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RT @SAFARI_ETH_CMU: Join us next week for two joint SAFARI-EFCL Seminars! @Hasindu2008 will present "Scalable, Efficient and Real-time Ana….
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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….
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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.
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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….
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RT @bach_warren: Congrats @Hasindu2008 and Nanopore Garvan team. This is an exciting development. I remember asking myself how AS might be….
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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.
Adaptively integrated sequencing and assembly of near-complete genomes #biorxiv_genomic.
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RT @naturemethods: Uncalled4: a toolkit for nanopore signal alignment, analysis and visualization of DNA and RNA modifications. https://t.….
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RT @lh3lh3: compleasm-0.2.7 released, supporting the latest BUSCO dataset. Also a new option --retrocopy for marking potential processed ps….
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We are doing a live online session on how you can use slorado to basecall nanopore data on AMD GPUs, organised by Australia'a Pawsey Centre. Will be relavent to anyone who have access to AMD GPUs too. You can still register for the event from here:
For those who want to run nanopore basecalling on the Australia'a @PawseyCentre supercomputer (or any other AMD GPU clusters in general):.
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RT @goekelab: We are happy to share that our SG-NEx manuscript (led by @chenying927, @nadia_davidson, @yukkeiwan and @JonathanGoeke), is no….
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For those who want to run nanopore basecalling on the Australia'a @PawseyCentre supercomputer (or any other AMD GPU clusters in general):.
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Introducing realfreq, a framework to calculate modification frequencies in real-time using @nanopore sequencing. Preprint: See poster below
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