ArticleGigaScience2025
The enduring advantages of the SLOW5 file format for raw nanopore sequencing data.
Article in GigaScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
3 citing papers in PubMed.
- Targeted long-read sequencing enables comprehensive analysis of the genetic and epigenetic landscape of inherited myopathies.Nature communications · 2026Article
- DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage.Nature communications · 2026Article
- Long-read sequencing technologies and bioinformatics: a new perspective for decoding DNA methylation modifications.Journal of translational medicine · 2026Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Nanopore sequencing is a widespread and important method in genomics science. The raw electrical current signal data from a typical nanopore sequencing experiment are large and complex. This can be stored in 2 alternative file formats that are presently supported: POD5 is a signal data file format used by default on instruments from Oxford Nanopore Technologies (ONT); SLOW5 is an open-source file format originally developed as an alternative to ONT's previous file format, which was known as FAST5. The choice of format may have important implications for the cost, speed, and simplicity of nanopore signal data analysis, management, and storage. To inform this choice, we present a comparative evaluation of POD5 versus SLOW5. We conducted benchmarking experiments assessing file size, analysis performance, and usability on a variety of different computer architectures. Binary SLOW5 (BLOW5) showed superior performance during sequential and nonsequential (random access) file reading on most systems, manifesting in faster, cheaper basecalling and other analysis, and we could find no instance in which POD5 file reading was significantly faster than BLOW5. We demonstrate that BLOW5 file writing is highly parallelizable, thereby meeting the demands of data acquisition on ONT instruments. Our analysis also identified differences in the complexity and stability of the software libraries for SLOW5 (slow5lib) and POD5 (pod5), including a large discrepancy in the number of underlying software dependencies, which may complicate the pod5 compilation process. In summary, many of the advantages originally conceived for SLOW5 remain relevant today, despite the replacement of FAST5 with POD5 as ONT's core file format.
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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 OpenQuestion graph.