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BMC Bioinformatics. 2018 Apr 12;19(1):135. doi: 10.1186/s12859-018-2139-9.

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis.

Author information

1
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
2
University of Massachusetts Medical School, Worcester, MA, 01655, USA.
3
Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
4
Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
5
Institute of Human Genetics, University of Duisburg-Essen, Essen, Germany.
6
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, 02215, USA.
7
Department of Bioinformatics, School of Life Sciences, Tongji University, Shanghai, 200092, China.
8
State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
9
Beijing Institute of Basic Medical Sciences, Beijing, China.
10
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. henry_long@dfci.harvard.edu.
11
Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. henry_long@dfci.harvard.edu.

Abstract

BACKGROUND:

RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology has led to the continuous development of new tools for every step of analysis from alignment to downstream pathway analysis. However, effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts.

RESULTS:

Using the workflow management system Snakemake we have developed a user friendly, fast, efficient, and comprehensive pipeline for RNA-seq analysis. VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis workflow that combines some of the most popular tools to take RNA-seq analysis from raw sequencing data, through alignment and quality control, into downstream differential expression and pathway analysis. VIPER has been created in a modular fashion to allow for the rapid incorporation of new tools to expand the capabilities. This capacity has already been exploited to include very recently developed tools that explore immune infiltrate and T-cell CDR (Complementarity-Determining Regions) reconstruction abilities. The pipeline has been conveniently packaged such that minimal computational skills are required to download and install the dozens of software packages that VIPER uses.

CONCLUSIONS:

VIPER is a comprehensive solution that performs most standard RNA-seq analyses quickly and effectively with a built-in capacity for customization and expansion.

KEYWORDS:

Analysis; Gene fusion; Immunological infiltrate; Pipeline; RNA-seq; Snakemake

PMID:
29649993
PMCID:
PMC5897949
DOI:
10.1186/s12859-018-2139-9
[Indexed for MEDLINE]
Free PMC Article

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