Interactive visualization of nanopore sequencing signal data with Squigualiser.

Motivation: Nanopore sequencing current signal data can be 'basecalled' into sequence information or analysed directly, with the capacity to identify diverse molecular features, such as DNA/RNA base modifications and secondary structures. However, raw signal data is large and complex, and there is a need for improved visualization strategies to facilitate signal analysis, exploration and tool development.

Results: Squigualiser (Squiggle visualiser) is a toolkit for intuitive, interactive visualization of sequence-aligned signal data, which currently supports both DNA and RNA sequencing data from Oxford Nanopore Technologies instruments.

Simulation of nanopore sequencing signal data with tunable parameters.

In silico simulation of high-throughput sequencing data is a technique used widely in the genomics field. However, there is currently a lack of effective tools for creating simulated data from nanopore sequencing devices, which measure DNA or RNA molecules in the form of time-series current signal data. Here, we introduce Squigulator, a fast and simple tool for simulation of realistic nanopore signal data.

Efficient end-to-end long-read sequence mapping using minimap2-fpga integrated with hardware accelerated chaining.

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.