Accelerated nanopore basecalling with SLOW5 data format

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 Nanopore’s Guppy basecaller that enables SLOW5 data access, resulting in performance improvements that are essential for scalable, affordable basecalling. ### Competing Interest Statement I.W.D. manages a fee-for-service sequencing facility at the Garvan Institute of Medical Research that is a customer of Oxford Nanopore Technologies but has no further financial relationship. H.G. & J.M.F. have previously received travel and accommodation expenses to speak at Oxford Nanopore Technologies conferences. H.G. and I.W.D. have paid consultant roles with Sequin PTY LTD. The authors declare no other competing financial or non-financial interests. The authors declare no other competing financial or non-financial interests.