Related Experiment Video
Updated: Jul 28, 2025
Nanopore DNA Sequencing for Metagenomic Soil Analysis
Published on: December 14, 2017
Accelerated nanopore basecalling with SLOW5 data format
Hiruna Samarakoon1,2,3, James M Ferguson1,2, Hasindu Gamaarachchi1,2,3
1Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia.
Motivation:
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 computing (HPC) and cloud environments.
Results:
SLOW5 permits highly efficient sequential data access, eliminating a potential 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.
Availability And Implementation:
Buttery-eel is available at https://github.com/Psy-Fer/buttery-eel.
