Ving
A software for visualization of deep sequencing signals

The script in this package was designed by Marc Descrimes (contact: marc.descrimes@curie.fr).
The current implementation was written by Marc Descrimes and Yousra Ben Zouari.

Version: beta 1.1

This program is a free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

Prerequisites

The script runs with R (>= 3.0.2).
R packages GenomicRanges and Rsamtools should be installed.
http://bioconductor.org/packages/release/bioc/html/Rsamtools.html
http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html

R is a multi-platform software, thus Ving works on any system where R can be installed.
Ving has been successfully tested on Ubuntu (>= 12.04.2), MacOSX 10.9 and Windows 7.
The provided documentation explains how to use Ving on a UNIX system.

Samtools should be up and running in order to create bam file indexes.
Index files must be in the same directory as bam files, with the default file name given by samtools.
Samtools are in the repositories of many distros. Go here for the freshest version:
http://samtools.sourceforge.net/

You should now be able to start using real data!

Examples of NGS signal visualization using Ving

Click here to download command lines and truncated bam and gff files used to produce the following figures.