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bioRxiv · 10.1101/2023.02.06.527365

Accelerated nanopore basecalling with SLOW5 data format

Samarakoon, H.·Ferguson, J. M.·Gamaarachchi, H.·Deveson, I. W.
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Abstract

Nanopore sequencing is emerging as a key pillar in the genomic technology landscape but computational constraints limiting its scalability remain to be overcome. The translation of raw current signal data into DNA or RNA sequence reads, known as basecalling, is a major friction in any nanopore sequencing workflow. Here, we exploit the advantages of the recently developed signal data format SLOW5 to streamline and accelerate nanopore basecalling on high-performance computer (HPC) and cloud environments. SLOW5 permits highly efficient sequential data access, eliminating a significant analysis bottleneck. To take advantage of this, we introduce Buttery-eel, an open-source wrapper for Oxford Nanopores Guppy basecaller that enables SLOW5 data access, resulting in performance improvements that are essential for scalable, affordable basecalling.

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Samarakoon, H., Ferguson, J. M., Gamaarachchi, H., Deveson, I. W.. 2023-02-07. Accelerated nanopore basecalling with SLOW5 data format. https://doi.org/10.1101/2023.02.06.527365

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