NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis

Bioinformatics. 2018 Jan 1;34(1):107-108. doi: 10.1093/bioinformatics/btx540.


Motivation: Next-generation sequencing is now an established method in genomics, and massive amounts of sequencing data are being generated on a regular basis. Analysis of the sequencing data is typically performed by lab-specific in-house solutions, but the agreement of results from different facilities is often small. General standards for quality control, reproducibility and documentation are missing.

Results: We developed NGS-pipe, a flexible, transparent and easy-to-use framework for the design of pipelines to analyze whole-exome, whole-genome and transcriptome sequencing data. NGS-pipe facilitates the harmonization of genomic data analysis by supporting quality control, documentation, reproducibility, parallelization and easy adaptation to other NGS experiments.

Availability and implementation:


Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Gene Expression Profiling / methods
  • Gene Expression Profiling / standards
  • Genomics / methods
  • High-Throughput Nucleotide Sequencing / methods*
  • High-Throughput Nucleotide Sequencing / standards
  • Humans
  • Neoplasms / genetics
  • Reproducibility of Results
  • Sequence Analysis, DNA / methods*
  • Sequence Analysis, DNA / standards
  • Sequence Analysis, RNA / methods*
  • Sequence Analysis, RNA / standards
  • Software*