Introduction

npReader is a tool to facilitate real-time conversion and analysis of Nanopore sequencing data. Its source code is part of Japsa package.

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

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.

3.Set the environment variable PATH to include the installation directory, eg,

set PATH=~/.usr/local/bin:$PATH

4.Usage information

jsa.np.f5reader --help

######On any OSs

1.Install JNI from https://www.hdfgroup.org/products/java/JNI/jhi5/index.html

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.

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.f5reader.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: doi: 10.1093/bioinformatics/btv658