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

Abstract

BackgroundRNA 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.ResultsUsing 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.ConclusionsVIPER is a comprehensive solution that performs most standard RNA-seq analyses quickly and effectively with a built-in capacity for customization and expansion.Electronic supplementary materialThe online version of this article (10.1186/s12859-018-2139-9) contains supplementary material, which is available to authorized users.

Sleeve Gastrectomy enhances glucose utilization and remodels adipose tissue independent of weight loss

“…[21,22] RNAseq analysis was performed using the VIPER snakemake pipeline. [23] The EnrichR platform was used to assess gene expression ontology. [24,25] Functional enrichment with WikiPathways 2019 Mouse and ChEA2016 Transcription pathway analysis are reported.…”

RNASeqR: An R Package for Automated Two-Group RNA-Seq Analysis Workflow

“…Galaxy [47], Taverna [48], Snakemake [49], Nextflow [50], CIPHER [51], and bcbio-nextgen [52] all provide NGS data analysis infrastructure in various computer language environments. For example, tools such as VIPER [2], TRAPLINE [53], HppRNA [54], and QuickRNASeq [55] are RNA-Seq pipelines based on the Snakemake framework, combining tools in numerous languages including R, Python, Perl, C++, or Java. Although there are many frameworks for RNA-Seq data analysis, only a few of them are able to run end-to-end RNA-Seq data analysis in a pure R environment.…”

RASflow: An RNA-Seq Analysis Workflow with Snakemake

“…As we can see from the table, some workflows do not include all the steps, either missing the QC steps [27,28], or the last steps, quantification and DEA [29]. Some of the workflows are limited to specific organisms typically human or mouse and in some cases other model organisms [30,27,31,32]. Some of them have functionality only for mapping reads to a reference genome and do not support the use of a transcriptome reference [27,31,32,33].…”

“…Some of the workflows are limited to specific organisms typically human or mouse and in some cases other model organisms [30,27,31,32]. Some of them have functionality only for mapping reads to a reference genome and do not support the use of a transcriptome reference [27,31,32,33]. Most of the workflows have high demands: some of them require a high-performance computer with large internal memory [31,29,32,33]; some of them need complex installation processes depending on the user to install other tools or libraries separately, which easily leads to version conflicts [28,33]; some workflows require users to be able to program which makes them unusable for some biologists [28,33].…”