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

Jochen Singer; Hans-Joachim Ruscheweyh; 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 Papassotiropoulos; Daniel J Stekhoven; Peter Wild; Thomas Wüst; Bernd Rinn; Niko Beerenwinkel

doi:10.1093/bioinformatics/btx540

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.

Authors

Jochen Singer^{1

2}, Hans-Joachim Ruscheweyh^{1

2

3}, Ariane L Hofmann^{1

2}, Thomas Thurnherr^{1

2}, Franziska Singer^{2

4}, Nora C Toussaint^{2

4}, Charlotte K Y Ng^{5

6

7}, Salvatore Piscuoglio⁸, Christian Beisel¹, Gerhard Christofori⁵, Reinhard Dummer⁹, Michael N Hall¹⁰, Wilhelm Krek¹¹, Mitchell P Levesque⁹, Markus G Manz¹², Holger Moch¹³, Andreas Papassotiropoulos^{14

15

16

17}, Daniel J Stekhoven^{2

4}, Peter Wild¹³, Thomas Wüst^{2

3}, Bernd Rinn^{2

3}, Niko Beerenwinkel^{1

2}

Affiliations

¹ Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
² SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
³ Scientific IT Services, ETH Zurich, Basel, Switzerland.
⁴ NEXUS Personalized Health Technologies, Zurich, Switzerland.
⁵ Department of Biomedicine, University of Basel, Basel, Switzerland.
⁶ Institute of Pathology.
⁷ Division of Gastroenterology and Hepatology, University Hospital Basel, Basel, Switzerland.
⁸ Institute of Pathology, University Hospital Basel, Basel, Switzerland.
⁹ Department of Dermatology, University Hospital Zurich, Zurich, Switzerland.
¹⁰ Biozentrum, University of Basel, Basel, Switzerland.
¹¹ Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
¹² Division of Hematology, University Hospital Zurich, Zurich, Switzerland.
¹³ Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland.
¹⁴ Division of Molecular Neuroscience, Department of Psychology.
¹⁵ Transfaculty Research Platform Molecular and Cognitive Neurosciences.
¹⁶ Psychiatric University Clinics University of Basel, Basel, Switzerland.
¹⁷ Department Biozentrum, Life Sciences Training Facility, University of Basel, Basel, Switzerland.

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.

Contact: niko.beerenwinkel@bsse.ethz.ch.

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*

Grants and funding

609883/ERC_/European Research Council/International