Automated processing of NGS data from raw sequencing files to ready-to-use information tables for genome modeling

  • Robert Deelen Johannes Gutenberg Universität of Mainz
  • Martin Wieland Johannes Gutenberg University Mainz
  • Susanne Gerber Johannes Gutenberg University Mainz
  • David Fournier Johannes Gutenberg Universität of Mainz

Abstract

Epigenetic features such as histone and DNA modifications are important mechanisms for the regulation of gene expression and for cell and tissue development. As a result, extensive efforts are currently undertaken using next-generation sequencing (NGS) to generate vast amounts of data regarding the epigenetic regulation of genomes. Several tools and frameworks for the processing of these NGS data have been developed in the last decade. Nevertheless, each user still bares the challenge to integrate all these tasks to perform the analysis. This procedure is not only tedious but also resource-intensive due to the putative large processing power involved. To automate, standardize and speed up the handling of NGS data, with focus on ChIP-seq data, we present a user-friendly pipeline that automatically processes a list of sequencing data files and returns a ready-to-use purified table for subsequent modelling or analysis attempts.

Published
2018-03-15
How to Cite
DEELEN, Robert et al. Automated processing of NGS data from raw sequencing files to ready-to-use information tables for genome modeling. Genomics and Computational Biology, [S.l.], v. 4, n. 2, p. e100042, mar. 2018. ISSN 2365-7154. Available at: <https://genomicscomputbiol.org/ojs3/GCB/article/view/42>. Date accessed: 25 june 2019. doi: https://doi.org/10.18547/gcb.2018.vol4.iss2.e100042.