GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis H Gamaarachchi, CW Lam, G Jayatilaka, H Samarakoon, JT Simpson, ... BMC bioinformatics 21, 1-13, 2020 | 84 | 2020 |
Fast nanopore sequencing data analysis with SLOW5 H Gamaarachchi, H Samarakoon, SP Jenner, JM Ferguson, TG Amos, ... Nature biotechnology 40 (7), 1026-1029, 2022 | 69 | 2022 |
Genopo: a nanopore sequencing analysis toolkit for portable Android devices H Samarakoon, S Punchihewa, A Senanayake, JM Hammond, ... Communications biology 3 (1), 538, 2020 | 21 | 2020 |
Flexible and efficient handling of nanopore sequencing signal data with slow5tools H Samarakoon, JM Ferguson, SP Jenner, TG Amos, S Parameswaran, ... Genome Biology 24 (1), 69, 2023 | 19 | 2023 |
Accelerated nanopore basecalling with SLOW5 data format H Samarakoon, JM Ferguson, H Gamaarachchi, IW Deveson Bioinformatics 39 (6), btad352, 2023 | 17 | 2023 |
Squigulator: simulation of nanopore sequencing signal data with tunable noise parameters H Gamaarachchi, JM Ferguson, H Samarakoon, K Liyanage, IW Deveson Biorxiv, 2023.05. 09.539953, 2023 | 9 | 2023 |
Interactive visualisation of raw nanopore signal data with Squigualiser H Samarakoon, K Liyanage, JM Ferguson, S Parameswaran, ... Biorxiv, 2024.02. 19.581111, 2024 | 4 | 2024 |
Strobilanthes medahinnensis (Acanthaceae) a new species, based on morphological and molecular data, from the Peak Wilderness Nature Reserve, Sri Lanka. RMR Nilanthi, H Samarakoon, N Jayawardana, S Wijesundara, ... | 4 | 2021 |
F5N : Nanopore Sequence Analysis Toolkit for Android Smartphones H Samarakoon, S Punchihewa, A Senanayake, R Ragel, ... bioRxiv, 2020.03. 22.002030, 2020 | 4 | 2020 |
Strobilanthes glandulata (Acanthaceae), a new species from Sri Lanka based on the morphological and molecular evidences RMR Nilanthi, H Samarakoon, N Jayawardana, B Hathurusinghe, ... Phytotaxa 573 (1), 1-14, 2022 | 3 | 2022 |
Efficient end-to-end long-read sequence mapping using minimap2-fpga integrated with hardware accelerated chaining K Liyanage, H Samarakoon, S Parameswaran, H Gamaarachchi Scientific Reports 13 (1), 20174, 2023 | 2 | 2023 |
Simulation of nanopore sequencing signal data with tunable parameters H Gamaarachchi, JM Ferguson, H Samarakoon, K Liyanage, IW Deveson Genome Research 34 (5), 778-783, 2024 | 1 | 2024 |
Chloroplast genome, nuclear ITS regions, mitogenome regions, and Skmer analysis resolved the genetic relationship among Cinnamomum species in Sri Lanka PCG Bandaranayake, N Naranpanawa, CB Chandrasekara, ... Plos one 18 (9), e0291763, 2023 | 1 | 2023 |
Accelerating Chaining in Genomic Analysis Using RISC-V Custom Instructions K Liyanage, H Gamaarachchi, H Saadat, T Li, H Samarakoon, ... 2024 Design, Automation & Test in Europe Conference & Exhibition (DATE), 1-6, 2024 | | 2024 |
Leveraging Basecaller's Move Table to Generate a Lightweight k-mer Model H Samarakoon, Y Kei Wan, S Parameswaran, J Göke, H Gamaarachchi, ... bioRxiv, 2024.06. 30.601452, 2024 | | 2024 |
minimap2-fpga: Integrating hardware-accelerated chaining for efficient end-to-end long-read sequence mapping K Liyanage, H Samarakoon, S Parameswaran, H Gamaarachchi bioRxiv, 2023.05. 30.542681, 2023 | | 2023 |
SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis H Gamaarachchi, H Samarakoon, SP Jenner, JM Ferguson, TG Amos, ... bioRxiv, 2021.06. 29.450255, 2021 | | 2021 |
Supplementary Materials: GPU Accelerated Adaptive Banded Event Alignment for Rapid Comparative Nanopore Signal Analysis H Gamaarachchi, CW Lam, G Jayatilaka, H Samarakoon, JT Simpson, ... | | |