Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Jan 1;34(1):107-108.
doi: 10.1093/bioinformatics/btx540.

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

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 Piscuoglio  8 , Christian Beisel  1 , Gerhard Christofori  5 , Reinhard Dummer  9 , Michael N Hall  10 , Wilhelm Krek  11 , Mitchell P Levesque  9 , Markus G Manz  12 , Holger Moch  13 , Andreas Papassotiropoulos  14   15   16   17 , Daniel J Stekhoven  2   4 , Peter Wild  13 , Thomas Wüst  2   3 , Bernd Rinn  2   3 , Niko Beerenwinkel  1   2
Affiliations

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

Jochen Singer et al. Bioinformatics. .

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.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1
Schematic overview of the different pre-configured pipelines available in NGS-pipe
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Alioto T.S. et al. (2015) A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat. Commun., 6, 10001.. - PMC - PubMed
    1. Aziz N. et al. (2015) College of american pathologists’ laboratory standards for next-generation sequencing clinical tests. Arch. Pathol. Lab. Med., 139, 481–493. - PubMed
    1. Denroche R.E. et al. (2015) A cancer cell-line titration series for evaluating somatic classification. BMC Res. Notes, 8, 823. - PMC - PubMed
    1. Hofmann A.L. et al. (2017) Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers. BMC Bioinformatics, 18, 8. - PMC - PubMed
    1. Koster J., Rahmann S. (2012) Snakemake–a scalable bioinformatics workflow engine. Bioinformatics, 28, 2520–2522. - PubMed

Publication types

MeSH terms