studyfranco / ngs-qc

NGS-QC Generator

About

Comparative analysis between ChIP-seq and other NGS datasets requires prior characterization of their degree of technical similarity. NGS Q/C Generator infer Quality indicators from the distribution of sequenced reads associated to a particular NGS profile. Such information is then used for comparative purposes and for defining strategies aiming to improve the quality of the sample-derived datasets.

Authors

Mendoza-Parra et. all

Improved and maintained by Matthias Blum and Pierre-Etienne Cholley.

Requirements

• sort from the GNU coreutils
• Python 2.7 and the following packages:
  • numpy
  • scipy (requires lapack-devel, and blas-devel)
  • matplotlib
  • Pillow (requires libzip-devel, libjpeg-devel, and libpng-devel)
  • reportlab
• Bedtools
• Gnuplot 4.4+ (requires libcairo2-dev, libgd2-xpm-dev, and libpango1.0-dev)

Installation

Build the C tools by running sh build.sh in the utils directory. Create a copy of config.ini.sample, rename it config.ini, and modify it (change the softwares section)