PLoS ONE: NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030619

NGS QC Toolkit provides tools for QC of Illumina and Roche 454 data and additional tools for conversion between NGS data formats, sequence trimming and statistics calculation. Various tools available in the NGS QC Toolkit along with their utility have been summarized in Figure 1. All the tools are equipped with user-friendly options and provide proper guidelines for running.

NGS QC Toolkit is a standalone and open source application freely available at http://www.nipgr.res.in/ngsqctoolkit.htm​l. Detailed description about installation and usage of the toolkit is available in user manual on the web site. In brief, to install the toolkit, user needs to download NGSQCToolkit_v2.2.zip (current version) file from the website and unzip it. Dependencies for using toolkit include Perl interpreter (usually supplied with OS for Linux and ActivePerl for Windows) and additional Perl modules, GD (optional; required to generate QC graphs) and String::Approx. Their installation instructions can be found on their respective websites.