Accelerated nanopore basecalling with SLOW5 data format.
Bioinformatics
; 39(6)2023 06 01.
Article
em En
| MEDLINE
| ID: mdl-37252813
ABSTRACT
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.
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Base de dados:
MEDLINE
Assunto principal:
Software
/
Nanoporos
Idioma:
En
Ano de publicação:
2023
Tipo de documento:
Article