ArticleBioinformatics (Oxford, England)2023
Accelerated nanopore basecalling with SLOW5 data format.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Targeted long-read sequencing enables comprehensive analysis of the genetic and epigenetic landscape of inherited myopathies.Nature communications · 2026Article
- Oxford Nanopore enhanced accuracy of long-read amplicons applied to microbial whole-genome sequencing.Microbiology spectrum · 2026Article
- Computational Metagenomics: State of the Art.International journal of molecular sciences · 2025Review
- Alternative polyadenylation and metabolic profiling in young panicle development of hybrid rice and its parents.Rice (New York, N.Y.) · 2025Article
- A new compression strategy to reduce the size of nanopore sequencing data.Genome research · 2025Article
- A genome assembly and annotation for the Australian alpine skink Bassiana duperreyi using long-read technologies.G3 (Bethesda, Md.) · 2025Article
- Targeted Long-Read Sequencing as a Single Assay Improves the Diagnosis of Spastic-Ataxia Disorders.Annals of clinical and translational neurology · 2025Article
- Realfreq: real-time base modification analysis for nanopore sequencing.Bioinformatics (Oxford, England) · 2025Article
- A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps.GigaScience · 2025Article
- The enduring advantages of the SLOW5 file format for raw nanopore sequencing data.GigaScience · 2025Article
- Decoding microbiome responses to quarantine potato wart disease: first insights into suppression and biocontrol by full-length 16S rRNA gene profiling and functional prediction.Frontiers in plant science · 2025Article
- Trends and characteristics of multidrug-resistant MRSA in Norway 2008-2020.Frontiers in microbiology · 2025Article
- End-to-end simulation of nanopore sequencing signals with feed-forward transformers.Bioinformatics (Oxford, England) · 2024Article
- A common flanking variant is associated with enhanced stability of the FGF14-SCA27B repeat locus.Nature genetics · 2024Article
- LINE-1 retrotransposons contribute to mouse PV interneuron development.Nature neuroscience · 2024Article
- Simulation of nanopore sequencing signal data with tunable parameters.Genome research · 2024Article
- Unveiling microbial diversity: harnessing long-read sequencing technology.Nature methods · 2024Review
- Streamlining remote nanopore data access with slow5curl.GigaScience · 2024Article
- Article
- Efficient end-to-end long-read sequence mapping using minimap2-fpga integrated with hardware accelerated chaining.Scientific reports · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationNanopore 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.
resultsSLOW5 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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.