npReader is a tool to facilitate real-time conversion and analysis of Nanopore sequencing data. It was developed as part of Japsa package where its source code and documentation reside.
######Under Linux/Mac
1.Install JHI5 using the packaging tool of your operating system distribution. For example, under Debian/Ubuntu
sudo apt-get install libjhdf5-jni
For MacOS, you can download and install hdfviewer from https://support.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdf-java-2.10.1/bin/
2.Obtain the source code, compile and install
git clone https://github.com/mdcao/japsa
cd japsa
make install JLP=/usr/lib/jni \
[INSTALL_DIR=~/.usr/local \]
[MXMEM=7000m \]
[SERVER=true \]
Change the JLP directive to point to where JHI5 is installed if needed. In a standard installation, the directive would be /usr/lib/jni for Linux or /Applications/HDFView.app/Content/Resources/lib for MacOS.
3.Set the environment variable PATH to include the installation directory, eg,
set PATH=~/.usr/local/bin:$PATH
4.Usage information
jsa.np.npreader --help
######On any OSs
1.Install hdf from https://support.hdfgroup.org/downloads/. The current version (1.7-02a) was tested with hdf version 2.10.1, which can be downloaded from https://support.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdf-java-2.10.1/bin/. During installation of hdf, please take note of where the library is installed.
2.Download pre-compiled Japsa of the latest release from https://github.com/mdcao/japsa/releases
3.Unzip the package, and run install.sh (for Linux/Mac) or install.bat (for Windows) and follow the prompt. Enter the path to hdf library when asked.
Detailed usage of npReader including setting up streaming analysis of nanopore sequencing in genuine real-time can be found from http://japsa.readthedocs.org/en/latest/tools/jsa.np.npreader.html
General information of Japsa can be found on its ReadTheDoc
If you find npReader useful for your research, please cite its publication:
Cao MD, Ganesamoorthy D, Cooper MA, Coin LJM, (2016). Realtime analysis and visualization of MinION sequencing data with npReader. Bioinformatics, 32(5):764–766. DOI:10.1093/bioinformatics/btv658