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

• DOI: 10.1093/bioinformatics/btx540
• Publication Date: 2017-08-26T11:08:23Z
• Authors: Jochen Singer; Hans-Joachim Rusc...; Ariane L Hofmann; Thomas Thurnherr; Franziska Singer; Nora C Toussaint; Charlotte K Y Ng; Salvatore Piscuoglio; Christian Beisel; Gerhard Christofori; Reinhard Dummer; Michael N Hall; Wilhelm Krek; Mitchell P Levesque; Markus G Manz; Holger Moch; Andreas Papassoti...; Daniel J Stekhoven; Peter Wild; Thomas Wüst; Bernd Rinn; Niko Beerenwinkel
• Keywords: Statistics and Probability; 0301 basic medicine; 1303 Biochemistry; 0206 medical engineering; 610 Medicine & health; 02 engineering and technology; Biochemistry; 03 medical and health sciences; 10049 Institute of Pathology and Molecular Pathology; Neoplasms; 1312 Molecular Biology; 1706 Computer Science Applications; Humans; 2613 Statistics and Probability; Molecular Biology; Sequence Analysis, RNA; Gene Expression Profiling; 10177 Dermatology Clinic; High-Throughput Nucleotide Sequencing; Reproducibility of Results; Genomics; Sequence Analysis, DNA; Applications Notes; Computer Science Applications; Computational Mathematics; Computational Theory and Mathematics; 10032 Clinic for Oncology and Hematology; 2605 Computational Mathematics; Software; 1703 Computational Theory and Mathematics

Abstract

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 https://github.com/cbg-ethz/NGS-pipe