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Introduction
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Publications
Publications (11)
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 visualisation strategies to faci...
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 si...
Nanopore sequencing measures ionic current during the translocation of DNA, RNA or protein molecules through a nanoscale protein pore. This raw current signal data can be ‘basecalled’ into sequence information and has the potential to identify other diverse molecular features, such as base modifications, secondary structures, etc. Despite the uniqu...
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 mappin...
DNA sequence analysis is a computationally intensive task. Minimap2 is a state-of-the-art software tool for third-generation sequence analysis workflow. Nearly 50% of Minimap2’s computation time is spent on what is known as the chaining step. In this article, the chaining step is accelerated using a novel heterogeneous computing system combining an...
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...
In silico simulation of next-generation sequencing data is a technique used widely in the genomics field. However, there is currently a lack of optimal tools for creating simulated data from 'third-generation' nanopore sequencing devices, which measure DNA or RNA molecules in the form of time-series current signal data. Here, we introduce Squigulat...
This work proposes a novel technique for hardware area-time estimation of applications on FPGA. The application C code is first converted to the target independent LLVM IR prior to wrapping the basic blocks as functions using a LLVM transformation pass. The LegUp tool’s ‘LLVM IR functions to RTL modules’ conversion is carried out to facilitate RTL...
