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A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
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NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis.

Jochen Singer1,2, Hans-Joachim Ruscheweyh1,2,3, Ariane L Hofmann1,2

  • 1Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.

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Summary

NGS-pipe is a new framework for analyzing next-generation sequencing (NGS) data. It improves data harmonization, quality control, and reproducibility across different genomic analysis facilities.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Next-generation sequencing (NGS) generates vast amounts of data.
  • Current analysis methods lack standardization, leading to poor reproducibility.
  • Quality control and documentation are often inconsistent across labs.

Purpose of the Study:

  • To develop a standardized framework for NGS data analysis.
  • To improve harmonization, quality control, and reproducibility in genomics.

Main Methods:

  • Developed NGS-pipe, a flexible and user-friendly pipeline framework.
  • The framework supports whole-exome, whole-genome, and transcriptome sequencing data analysis.
  • Incorporates features for quality control, documentation, and parallelization.

Main Results:

  • NGS-pipe provides a transparent and adaptable solution for genomic data analysis.
  • Facilitates harmonization of results across different sequencing facilities.
  • Enhances reproducibility and simplifies the adaptation to new NGS experiments.

Conclusions:

  • NGS-pipe addresses the need for standardized NGS data analysis.
  • It offers a robust framework to improve the reliability and comparability of genomic research.
  • The tool is available for broad adoption in the scientific community.