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

Content Provider	Springer Nature : BioMed Central
Author	Gamaarachchi, Hasindu Lam, Chun Wai Jayatilaka, Gihan Samarakoon, Hiruna Simpson, Jared T. Smith, Martin A. Parameswaran, Sri
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 .
Related Links	https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-03697-x.pdf
Ending Page	13
Page Count	13
Starting Page	1
File Format	HTM / HTML
ISSN	14712105
DOI	10.1186/s12859-020-03697-x
Journal	BMC Bioinformatics
Issue Number	1
Volume Number	21
Language	English
Publisher	BioMed Central
Publisher Date	2020-08-05
Access Restriction	Open
Subject Keyword	Bioinformatics Microarrays Computational Biology Computer Appl. in Life Sciences Algorithms Nanopore Signal alignment Event alignment Methylation GPU GPU acceleration Optimisation SoC Nanopolish f5c Computational Biology/Bioinformatics
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biochemistry Computer Science Applications Applied Mathematics Structural Biology
Journal Impact Factor	2.9/2023
5-Year Journal Impact Factor	3.6/2023

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