Title |
Realtime analysis and visualization of MinION sequencing data with npReader
|
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Published in |
Bioinformatics, November 2015
|
DOI | 10.1093/bioinformatics/btv658 |
Pubmed ID | |
Authors |
Minh Duc Cao, Devika Ganesamoorthy, Matthew A Cooper, Lachlan J M Coin |
Abstract |
The recently released Oxford Nanopore MinION sequencing platform presents many innovative features opening up potential for a range of applications not previously possible. Among these features, the ability to sequence in real-time provides a unique opportunity for many time-critical applications. While many software packages have been developed to analyse its data, there is still a lack of toolkits that support the streaming and real-time analysis of MinION sequencing data. We developed npReader, an open-source software package to facilitate real-time analysis of MinION sequencing data. npReader can simultaneously extract sequence reads and stream them to downstream analysis pipelines while the samples are being sequenced on the MinION device. It provides a command line interface for easy integration into a bioinformatics work flow, as well as a graphical user interface which concurrently displays the statistics of the run. It also provides an application programming interface for development of streaming algorithms in order to fully utilize the extent of nanopore sequencing potential. npReader is written in Java and is freely available at https://github.com/mdcao/npReader. Minh Duc Cao ([email protected]) and Lachlan J. M. Coin ([email protected]). |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 9 | 33% |
United Kingdom | 3 | 11% |
India | 2 | 7% |
Australia | 1 | 4% |
France | 1 | 4% |
Italy | 1 | 4% |
Sao Tome and Principe | 1 | 4% |
Israel | 1 | 4% |
Unknown | 8 | 30% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 14 | 52% |
Scientists | 13 | 48% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 2 | 2% |
Brazil | 2 | 2% |
Portugal | 1 | 1% |
Switzerland | 1 | 1% |
Italy | 1 | 1% |
France | 1 | 1% |
Netherlands | 1 | 1% |
Czechia | 1 | 1% |
Sweden | 1 | 1% |
Other | 2 | 2% |
Unknown | 84 | 87% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 38 | 39% |
Student > Master | 13 | 13% |
Student > Ph. D. Student | 11 | 11% |
Other | 9 | 9% |
Student > Bachelor | 6 | 6% |
Other | 11 | 11% |
Unknown | 9 | 9% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 35 | 36% |
Biochemistry, Genetics and Molecular Biology | 21 | 22% |
Computer Science | 13 | 13% |
Medicine and Dentistry | 6 | 6% |
Engineering | 2 | 2% |
Other | 6 | 6% |
Unknown | 14 | 14% |