Imperial College London
Alternate

DrLachlanCoin

Faculty of Medicine, Department of Infectious Disease

Honorary Senior Lecturer
 
 
 
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Contact

 

+44 (0)20 7594 1930l.coin

 
 
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Location

 

172Medical SchoolSt Mary's Campus

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Summary

 

Publications

Citation

BibTex format

@article{Minh:2015:bioinformatics/btv658,
author = {Minh, DC and Ganesamoorthy, D and Cooper, MA and Coin, LJM},
doi = {bioinformatics/btv658},
journal = {Bioinformatics},
pages = {764--766},
title = {Realtime analysis and visualization of MinION sequencing data with npReader},
url = {http://dx.doi.org/10.1093/bioinformatics/btv658},
volume = {32},
year = {2015}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - 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.Availability and implementation: npReader is written in Java and is freely available at https://github.com/mdcao/npReader.
AU  - Minh,DC
AU  - Ganesamoorthy,D
AU  - Cooper,MA
AU  - Coin,LJM
DO  - bioinformatics/btv658
EP  - 766
PY  - 2015///
SN  - 1367-4803
SP  - 764
TI  - Realtime analysis and visualization of MinION sequencing data with npReader
T2  - Bioinformatics
UR  - http://dx.doi.org/10.1093/bioinformatics/btv658
UR  - http://hdl.handle.net/10044/1/34196
VL  - 32
ER  -
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