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Flexible and efficient handling of nanopore sequencing signal data with slow5tools.

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.

SUBMITTER: Samarakoon H

PROVIDER: S-EPMC10080837 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature

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Flexible and efficient handling of nanopore sequencing signal data with slow5tools.

Samarakoon Hiruna H Ferguson James M JM Jenner Sasha P SP Amos Timothy G TG Parameswaran Sri S Gamaarachchi Hasindu H Deveson Ira W IW

Genome biology 20230406 1

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 conversio ...[more]

PMID: 37024927

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