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GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis

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Abstract

Background: Nanopore sequencing enables portable, real-time sequencing applications, including point-of-care diagnostics and in-the-field genotyping. Achieving these outcomes requires efficient bioinformatic algorithms for the analysis of raw nanopore signal data. However, comparing raw nanopore signals to a biological reference sequence is a computationally complex task. The dynamic programming algorithm called Adaptive Banded Event Alignment (ABEA) is a crucial step in polishing sequencing data and identifying non-standard nucleotides, such as measuring DNA methylation. Here, we parallelise and optimise an implementation of the ABEA algorithm (termed f5c) to efficiently run on heterogeneous CPU-GPU architectures. Results: By optimising memory, computations and load balancing between CPU and GPU, we demonstrate how f5c can perform ∼3-5 × faster than an optimised version of the original CPU-only implementation of ABEA in the Nanopolish software package. We also show that f5c enables DNA methylation detection on-the-fly using an embedded System on Chip (SoC) equipped with GPUs. Conclusions: Our work not only demonstrates that complex genomics analyses can be performed on lightweight computing systems, but also benefits High-Performance Computing (HPC). The associated source code for f5c along with GPU optimised ABEA is available at https://github.com/hasindu2008/f5c.

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APA

Gamaarachchi, H., Lam, C. W., Jayatilaka, G., Samarakoon, H., Simpson, J. T., Smith, M. A., & Parameswaran, S. (2020). GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis. BMC Bioinformatics, 21(1). https://doi.org/10.1186/s12859-020-03697-x

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