Fast nanopore sequencing data analysis with SLOW5.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 34980914.
- Also identified by DOI 10.1038/s41587-021-01147-4 and PMC identifier 9287168.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Nanopore sequencing depends on the FAST5 file format, which does not allow efficient parallel analysis. Here we introduce SLOW5, an alternative format engineered for efficient parallelization and acceleration of nanopore data analysis. Using the example of DNA methylation profiling of a human genome, analysis runtime is reduced from more than two weeks to approximately 10.5 h on a typical high-performance computer. SLOW5 is approximately 25% smaller than FAST5 and delivers consistent improvements on different computer architectures.
Medical subject headings
- Nanopore Sequencing
- Nanopores