Kisaru Liyanage

Open-source, Hardware-Independent GPU Acceleration for Scalable Nanopore Basecalling with Slorado and Openfish

This paper introduces open-source GPU-accelerated basecalling tools for nanopore sequencing that are hardware-independent and competitive with proprietary solutions.

Squigulator: simulation of nanopore sequencing signal data with tunable noise parameters

Squigulator simulates nanopore sequencing signals with tunable noise parameters to test and improve analysis methods.

Interactive visualisation of raw nanopore signal data with Squigualiser

Squigualiser provides an interactive visualization tool for nanopore signal data, enabling alignment to reference genomes and comparison of multiple datasets.

minimap2-fpga: Integrating hardware-accelerated chaining for efficient end-to-end long-read sequence mapping

The paper introduces minimap2-fpga, a hardware-accelerated version of minimap2 that improves mapping speed for long-read sequencing data with minimal accuracy loss.