ORCID Profile
0000-0002-5812-1046
Current Organisations
Garvan Institute of Medical Research
,
University of New South Wales
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Publisher: Oxford University Press (OUP)
Date: 30-05-2023
DOI: 10.1093/BIOINFORMATICS/BTAD352
Abstract: Nanopore sequencing is emerging as a key pillar in the genomic technology landscape but computational constraints limiting its scalability remain to be overcome. The translation of raw current signal data into DNA or RNA sequence reads, known as ‘basecalling’, is a major friction in any nanopore sequencing workflow. Here, we exploit the advantages of the recently developed signal data format ‘SLOW5’ to streamline and accelerate nanopore basecalling on high-performance computing (HPC) and cloud environments. SLOW5 permits highly efficient sequential data access, eliminating a potential analysis bottleneck. To take advantage of this, we introduce Buttery-eel, an open-source wrapper for Oxford Nanopore’s Guppy basecaller that enables SLOW5 data access, resulting in performance improvements that are essential for scalable, affordable basecalling. Buttery-eel is available at github.com/Psy-Fer/buttery-eel.
Publisher: Magnolia Press
Date: 17-11-2022
DOI: 10.11646/PHYTOTAXA.573.1.1
Abstract: Strobilanthes glandulata, a new species of Acanthaceae is described from Sri Lanka. It has been previously misidentified as Strobilanthes lupulina. It is similar to S. lupulina having an inflorescence of heads, funnel-shaped gradually widened corolla, hispids on the stem, and both surfaces of leaves and petioles, but can be easily distinguished from the latter by having different pollens, bracts arranged in well-spaced, margin crenate, and densely covered with glandular-hairy. The phylogenetic analyses indicate that it is a member of the native species of the genus Strobilanthes in Sri Lanka. A full description, detailed illustrations, pollen morphology, and complete chloroplast genome are provided.
Publisher: Cold Spring Harbor Laboratory
Date: 02-06-2023
DOI: 10.1101/2023.05.30.542681
Abstract: minimap2 is the gold-standard software for reference-based sequence mapping in third-generation long-read sequencing. While minimap2 is relatively fast, further speedup is desirable, especially when processing a multitude of large datasets. In this work, we present minimap2-fpga , a hardware-accelerated version of minimap2 that speeds up the mapping process by integrating an FPGA kernel optimised for chaining. We demonstrate speed-ups in end-to-end run-time for data from both Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio). minimap2-fpga is up to 79% and 53% faster than minimap2 for ∼ 30× ONT and ∼ 50× PacBio datasets respectively, when mapping without base-level alignment. When mapping with base-level alignment, minimap2-fpga is up to 62% and 10% faster than minimap2 for ∼ 30× ONT and ∼ 50× PacBio datasets respectively. The accuracy is near-identical to that of original minimap2 for both ONT and PacBio data, when mapping both with and without base-level alignment. minimap2-fpga is supported on Intel FPGA-based systems (evaluations performed on an on-premise system) and Xilinx FPGA-based systems (evaluations performed on a cloud system). We also provide a well-documented library for the FPGA-accelerated chaining kernel to be used by future researchers developing sequence alignment software with limited hardware background.
Publisher: Springer Science and Business Media LLC
Date: 03-01-2022
DOI: 10.1038/S41587-021-01147-4
Abstract: Nanopore sequencing depends on the FAST5 file format, which does not allow efficient parallel analysis. Here we introduce SLOW5, an alternative format engineered for efficient parallelization and acceleration of nanopore data analysis. Using the ex le of DNA methylation profiling of a human genome, analysis runtime is reduced from more than two weeks to approximately 10.5 h on a typical high-performance computer. SLOW5 is approximately 25% smaller than FAST5 and delivers consistent improvements on different computer architectures.
Publisher: Cold Spring Harbor Laboratory
Date: 20-06-2022
DOI: 10.1101/2022.06.19.496732
Abstract: Nanopore sequencing is an emerging technology that is being rapidly adopted in research and clinical genomics. We recently developed SLOW5, a new file format for storage and analysis of raw data from nanopore sequencing experiments. SLOW5 is a community-centric, open source format that offers considerable performance benefits over the existing nanopore data format, known as FAST5. Here we introduce slow5tools , a simple, intuitive toolkit for handling nanopore raw signal data in SLOW5 format. Slow5tools enables lossless FAST5-to-SLOW5 and SLOW5-to-FAST5 data conversion, and a range of tools for structuring, indexing, viewing and querying SLOW5 files. Slow5tools uses multi-threading, multi-processing and other engineering strategies to achieve fast data conversion and manipulation, including live FAST5-to-SLOW5 conversion during sequencing. We outline a series of ex les and benchmarking experiments to illustrate slow5tools usage, and describe the engineering principles underpinning its high performance. Slow5tools is an essential toolkit for handling nanopore signal data, which was developed to support adoption of SLOW5 by the nanopore community. Slow5tools is written in C/C++ with minimal dependencies and is freely available as an open-source program under an MIT licence: asindu2008/slow5tools .
Publisher: Cold Spring Harbor Laboratory
Date: 30-06-2021
DOI: 10.1101/2021.06.29.450255
Abstract: Nanopore sequencing is an emerging genomic technology with great potential. However, the storage and analysis of nanopore sequencing data have become major bottlenecks preventing more widespread adoption in research and clinical genomics. Here, we elucidate an inherent limitation in the file format used to store raw nanopore data – known as FAST5 – that prevents efficient analysis on high-performance computing (HPC) systems. To overcome this, we have developed SLOW5, an alternative file format that permits efficient parallelisation and, thereby, acceleration of nanopore data analysis. For ex le, we show that using SLOW5 format, instead of FAST5, reduces the time and cost of genome-wide DNA methylation profiling by an order of magnitude on common HPC systems, and delivers consistent improvements on a wide range of different architectures. With a simple, accessible file structure and a ~ 25% reduction in size compared to FAST5, SLOW5 format will deliver substantial benefits to all areas of the nanopore community.
Publisher: Magnolia Press
Date: 10-08-2021
DOI: 10.11646/PHYTOTAXA.514.1.2
Abstract: Strobilanthes medahinnensis, a new species of Acanthaceae is described and illustrated from Sri Lanka. The new species is similar to S. anceps in having ovate leaves, yellow gland dots of abaxial leaf surface and reflexed bracts but differs by rounded stem, leaves with acuminate apex, elongated spikes, lanceolate outermost bract with long acuminate apex. The establishment of the new species is supported by complete plastome genome analyses.
Publisher: Springer Science and Business Media LLC
Date: 29-09-2020
DOI: 10.1038/S42003-020-01270-Z
Abstract: The advent of portable nanopore sequencing devices has enabled DNA and RNA sequencing to be performed in the field or the clinic. However, advances in in situ genomics require parallel development of portable, offline solutions for the computational analysis of sequencing data. Here we introduce Genopo , a mobile toolkit for nanopore sequencing analysis. Genopo compacts popular bioinformatics tools to an Android application, enabling fully portable computation. To demonstrate its utility for in situ genome analysis, we use Genopo to determine the complete genome sequence of the human coronavirus SARS-CoV-2 in nine patient isolates sequenced on a nanopore device, with Genopo executing this workflow in less than 30 min per s le on a range of popular smartphones. We further show how Genopo can be used to profile DNA methylation in a human genome s le, illustrating a flexible, efficient architecture that is suitable to run many popular bioinformatics tools and accommodate small or large genomes. As the first ever smartphone application for nanopore sequencing analysis, Genopo enables the genomics community to harness this cheap, ubiquitous computational resource.
Publisher: Cold Spring Harbor Laboratory
Date: 24-03-2020
DOI: 10.1101/2020.03.22.002030
Abstract: F5N is the first ever Android application for nanopore sequence analysis on a mobile phone, comprised of popular tools for read alignment ( Minimap2 ), sequence data manipulation ( Samtools ) and methylation calling ( F5C/Nanopolish ). On NA12878 nanopore data, F5N can perform a complete methylation calling pipeline on a mobile phone in ∼15 minutes for a batch of 4000 nanopore reads (∼34 megabases). F5N is not only a toolkit but also a framework for integrating existing C/C++ based command line tools to run on Android. F5N will enable performing nanopore sequence analysis on-site when used with an ultra-portable nanopore sequencer (eg: MinION or the anticipated smidgION), consequently reducing the cost for special computers and high-speed Internet. F5N Android application is available on Google Play store at tore/apps/details?id=com.mobilegenomics.genopo& hl=en and the source code is available on Github at github.com/SanojPunchihewa/f5n . hirunas@eng.pdn.ac.lk
No related grants have been discovered for Hiruna Samarakoon.