Flexible and efficient handling of nanopore sequencing signal data with slow5tools

Hiruna Samarakoon; James M Ferguson; Sasha P Jenner; Timothy G Amos; Sri Parameswaran; Hasindu Gamaarachchi; Ira W Deveson

doi:10.1186/s13059-023-02910-3

Flexible and efficient handling of nanopore sequencing signal data with slow5tools

Genome Biol. 2023 Apr 6;24(1):69. doi: 10.1186/s13059-023-02910-3.

Authors

Hiruna Samarakoon^{1

2

3}, James M Ferguson^{1

2}, Sasha P Jenner^{1

2}, Timothy G Amos^{1

2}, Sri Parameswaran³, Hasindu Gamaarachchi^#^{4

5

6}, Ira W Deveson^#^{7

8

9}

Affiliations

¹ Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia.
² Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia.
³ School of Computer Science and Engineering, University of New South Wales, Sydney, NSW, Australia.
⁴ Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia. hasindu@garvan.org.au.
⁵ Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia. hasindu@garvan.org.au.
⁶ School of Computer Science and Engineering, University of New South Wales, Sydney, NSW, Australia. hasindu@garvan.org.au.
⁷ Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia. i.deveson@garvan.org.au.
⁸ Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia. i.deveson@garvan.org.au.
⁹ Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia. i.deveson@garvan.org.au.

^# Contributed equally.

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.

Keywords: Nanopore sequencing; Nanopore signal data; SLOW5; Toolkit.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genomics
High-Throughput Nucleotide Sequencing
Nanopore Sequencing*
Nanopores*
Sequence Analysis, DNA
Software