Title |
Flexible and efficient handling of nanopore sequencing signal data with slow5tools
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Published in |
Genome Biology, April 2023
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DOI | 10.1186/s13059-023-02910-3 |
Pubmed ID | |
Authors |
Hiruna Samarakoon, James M. Ferguson, Sasha P. Jenner, Timothy G. Amos, Sri Parameswaran, Hasindu Gamaarachchi, Ira W. Deveson |
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. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United States | 7 | 20% |
Australia | 5 | 14% |
United Kingdom | 4 | 11% |
France | 3 | 9% |
New Zealand | 2 | 6% |
Netherlands | 2 | 6% |
Finland | 1 | 3% |
Canada | 1 | 3% |
Switzerland | 1 | 3% |
Other | 0 | 0% |
Unknown | 9 | 26% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 21 | 60% |
Members of the public | 13 | 37% |
Practitioners (doctors, other healthcare professionals) | 1 | 3% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 21 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 7 | 33% |
Student > Bachelor | 3 | 14% |
Unspecified | 2 | 10% |
Student > Master | 2 | 10% |
Student > Doctoral Student | 1 | 5% |
Other | 3 | 14% |
Unknown | 3 | 14% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 7 | 33% |
Unspecified | 2 | 10% |
Agricultural and Biological Sciences | 2 | 10% |
Computer Science | 1 | 5% |
Physics and Astronomy | 1 | 5% |
Other | 3 | 14% |
Unknown | 5 | 24% |