Format

Send to

Choose Destination
G3 (Bethesda). 2019 Jul 9;9(7):2089-2096. doi: 10.1534/g3.119.400185.

ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data.

Author information

1
SIB Swiss Institute of Bioinformatics, Zurich, Switzerland.
2
Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
3
Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
4
Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
5
SIB Swiss Institute of Bioinformatics, Zurich, Switzerland mark.robinson@imls.uzh.ch charlotte.soneson@fmi.ch.

Abstract

The extensive generation of RNA sequencing (RNA-seq) data in the last decade has resulted in a myriad of specialized software for its analysis. Each software module typically targets a specific step within the analysis pipeline, making it necessary to join several of them to get a single cohesive workflow. Multiple software programs automating this procedure have been proposed, but often lack modularity, transparency or flexibility. We present ARMOR, which performs an end-to-end RNA-seq data analysis, from raw read files, via quality checks, alignment and quantification, to differential expression testing, geneset analysis and browser-based exploration of the data. ARMOR is implemented using the Snakemake workflow management system and leverages conda environments; Bioconductor objects are generated to facilitate downstream analysis, ensuring seamless integration with many R packages. The workflow is easily implemented by cloning the GitHub repository, replacing the supplied input and reference files and editing a configuration file. Although we have selected the tools currently included in ARMOR, the setup is modular and alternative tools can be easily integrated.

KEYWORDS:

Differential expression; Exploratory data analysis; Quality control; RNA sequencing

Supplemental Content

Full text links

Icon for HighWire Icon for PubMed Central
Loading ...
Support Center