Introduction

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.

Quick installation guide

######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/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.

Documentation

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

Reference

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