Flexible and efficient handling of nanopore sequencing signal data with slow5tools

被引：0

作者：

Hiruna Samarakoon

James M. Ferguson

Sasha P. Jenner

Timothy G. Amos

Sri Parameswaran

Hasindu Gamaarachchi

Ira W. Deveson

机构：

[1] Garvan Institute of Medical Research,Genomics Pillar

[2] Garvan Institute of Medical Research and Murdoch Children’s Research Institute,Centre for Population Genomics

[3] University of New South Wales,School of Computer Science and Engineering

[4] University of New South Wales,Faculty of Medicine

来源：

Genome Biology | / 24卷

关键词：

Nanopore sequencing; Nanopore signal data; SLOW5; Toolkit;

D O I：

暂无

中图分类号：

学科分类号：

摘要：

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.

引用

共 19 条

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