ArticleGenome biology2023
Flexible and efficient handling of nanopore sequencing signal data with slow5tools.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Centromeric retrotransposons shape chromosomal evolution beyond pericentromeric regions.Mobile DNA · 2026Article
- Skin Colour in Salamanders Is Modulated by Both Epitranscriptomic Methylation and Gene Expression.Molecular ecology · 2026Article
- A dual context-aware basecaller for nanopore direct RNA sequencing.Nature communications · 2026Article
- Comprehensive mapping of RNA modification dynamics and crosstalk via deep learning and nanopore direct RNA-sequencing.Nature communications · 2026Article
- A whole-genome sequencing dataset of nanopore raw signals for bacterial genotyping and methylation analysis.Scientific data · 2025Article
- A new compression strategy to reduce the size of nanopore sequencing data.Genome research · 2025Article
- Characterisation of the ABO Blood Group Phenotypes Using Third-Generation Sequencing.International journal of molecular sciences · 2025Article
- A genome assembly and annotation for the Australian alpine skink Bassiana duperreyi using long-read technologies.G3 (Bethesda, Md.) · 2025Article
- Leveraging basecaller's move table to generate a lightweight k-mer model for nanopore sequencing analysis.Bioinformatics (Oxford, England) · 2025Article
- Interactive visualization of nanopore sequencing signal data with Squigualiser.Bioinformatics (Oxford, England) · 2024Article
- A common flanking variant is associated with enhanced stability of the FGF14-SCA27B repeat locus.Nature genetics · 2024Article
- Simulation of nanopore sequencing signal data with tunable parameters.Genome research · 2024Article
- Comparison of CcrM-dependent methylation inJournal of bacteriology · 2024Article
- Nanopore Current Events Magnifier (nanoCEM): a novel tool for visualizing current events at modification sites of nanopore sequencing.NAR genomics and bioinformatics · 2024Article
- Narrowing the diagnostic gap: Genomes, episignatures, long-read sequencing, and health economic analyses in an exome-negative intellectual disability cohort.Genetics in medicine : official journal of the American College of Medical Genetics · 2024Article
- EpiDiP/NanoDiP: a versatile unsupervised machine learning edge computing platform for epigenomic tumour diagnostics.Acta neuropathologica communications · 2024Article
- Extensive DNA methylome rearrangement during early lamprey embryogenesis.Nature communications · 2024Article
- Comparison of CcrM-dependent methylation inbioRxiv : the preprint server for biology · 2024Article
- Streamlining remote nanopore data access with slow5curl.GigaScience · 2024Article
- Cold Tumour Phenotype Explained Through Whole Genome Sequencing in Clinical Nasopharyngeal Cancer: A Preliminary Study.ImmunoTargets and therapy · 2024Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nanopore sequencing is being rapidly adopted in genomics. We recently developed SLOW5, a new file format with advantages for storage and analysis of raw signal data from nanopore experiments. Here we introduce slow5tools, an intuitive toolkit for handling nanopore data in SLOW5 format. Slow5tools enables lossless data conversion and a range of tools for interacting with SLOW5 files. Slow5tools uses multi-threading, multi-processing, and other engineering strategies to achieve fast data conversion and manipulation, including live FAST5-to-SLOW5 conversion during sequencing. We provide examples and benchmarking experiments to illustrate slow5tools usage, and describe the engineering principles underpinning its performance.
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Registered trials
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 Socratic graph.