Fast nanopore sequencing data analysis with SLOW5.
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ABSTRACT:
SUBMITTER: Gamaarachchi H
PROVIDER: S-EPMC9287168 | biostudies-literature | 2022 Jul
REPOSITORIES: biostudies-literature
Publications
Fast nanopore sequencing data analysis with SLOW5.
Gamaarachchi Hasindu H Samarakoon Hiruna H Jenner Sasha P SP Ferguson James M JM Amos Timothy G TG Hammond Jillian M JM Saadat Hassaan H Smith Martin A MA Parameswaran Sri S Deveson Ira W IW
Nature biotechnology 20220103 7
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 improvement ...[more]
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