Fast nanopore sequencing data analysis with SLOW5

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...

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Detalles Bibliográficos
Autores principales: Gamaarachchi, Hasindu, Samarakoon, Hiruna, Jenner, Sasha P., Ferguson, James M., Amos, Timothy G., Hammond, Jillian M., Saadat, Hassaan, Smith, Martin A., Parameswaran, Sri, Deveson, Ira W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group US 2022
Materias:
Brief Communication
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9287168/
https://www.ncbi.nlm.nih.gov/pubmed/34980914
http://dx.doi.org/10.1038/s41587-021-01147-4
Descripción
Sumario: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.

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