Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia.
Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia.
Genome Biol. 2023 Apr 6;24(1):69. doi: 10.1186/s13059-023-02910-3.
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.
纳米孔测序技术在基因组学领域得到了迅速应用。我们最近开发了 SLOW5，这是一种新的文件格式，在存储和分析纳米孔实验原始信号数据方面具有优势。在这里，我们介绍了 slow5tools，这是一个直观的工具包，用于处理 SLOW5 格式的纳米孔数据。slow5tools 支持无损数据转换和一系列用于与 SLOW5 文件交互的工具。slow5tools 使用多线程、多进程和其他工程策略来实现快速的数据转换和操作，包括在测序过程中实时的 FAST5 到 SLOW5 转换。我们提供了示例和基准测试实验来说明 slow5tools 的用法，并描述了支持其性能的工程原理。
