Realtime analysis and visualisation of MinION sequencing data with npReader

Cao, Minh Duc, Ganesamoorthy, Devika, Cooper, Matthew A. and Coin, Lachlan J.M. (2015) Realtime analysis and visualisation of MinION sequencing data with npReader. Bioinformatics, 32 5: 764-766. doi:10.1093/bioinformatics/btv658

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Author Cao, Minh Duc
Ganesamoorthy, Devika
Cooper, Matthew A.
Coin, Lachlan J.M.
Title Realtime analysis and visualisation of MinION sequencing data with npReader
Journal name Bioinformatics   Check publisher's open access policy
ISSN 1460-2059
Publication date 2015-11-01
Year available 2015
Sub-type Article (original research)
DOI 10.1093/bioinformatics/btv658
Open Access Status DOI
Volume 32
Issue 5
Start page 764
End page 766
Total pages 3
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Formatted abstract
Motivation: 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 analyze its data, there is still a lack of toolkits that support the streaming and real-time analysis of MinION sequencing data.

Results: 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.
Keyword Biochemical Research Methods
Biotechnology & Applied Microbiology
Computer Science, Interdisciplinary Applications
Mathematical & Computational Biology
Statistics & Probability
Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Computer Science
Mathematical & Computational Biology
Q-Index Code CX
Q-Index Status Provisional Code
Grant ID GNT1052303
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
Institute for Molecular Bioscience - Publications
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Citation counts: TR Web of Science Citation Count  Cited 4 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 4 times in Scopus Article | Citations
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Created: Wed, 09 Dec 2015, 19:06:31 EST by Susan Allen on behalf of Institute for Molecular Bioscience