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. 2016 Sep 20:17:388.
doi: 10.1186/s12859-016-1241-0.

systemPipeR: NGS workflow and report generation environment

Tyler W H Backman  1 , Thomas Girke  2
Affiliations

systemPipeR: NGS workflow and report generation environment

Tyler W H Backman et al. BMC Bioinformatics. .

Abstract

Background: Next-generation sequencing (NGS) has revolutionized how research is carried out in many areas of biology and medicine. However, the analysis of NGS data remains a major obstacle to the efficient utilization of the technology, as it requires complex multi-step processing of big data demanding considerable computational expertise from users. While substantial effort has been invested on the development of software dedicated to the individual analysis steps of NGS experiments, insufficient resources are currently available for integrating the individual software components within the widely used R/Bioconductor environment into automated workflows capable of running the analysis of most types of NGS applications from start-to-finish in a time-efficient and reproducible manner.

Results: To address this need, we have developed the R/Bioconductor package systemPipeR. It is an extensible environment for both building and running end-to-end analysis workflows with automated report generation for a wide range of NGS applications. Its unique features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software on local computers and computer clusters. A flexible sample annotation infrastructure efficiently handles complex sample sets and experimental designs. To simplify the analysis of widely used NGS applications, the package provides pre-configured workflows and reporting templates for RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Additional workflow templates will be provided in the future.

Conclusions: systemPipeR accelerates the extraction of reproducible analysis results from NGS experiments. By combining the capabilities of many R/Bioconductor and command-line tools, it makes efficient use of existing software resources without limiting the user to a set of predefined methods or environments. systemPipeR is freely available for all common operating systems from Bioconductor ( http://bioconductor.org/packages/devel/systemPipeR ).

Keywords: Analysis workflow; ChIP-Seq; Next Generation Sequencing (NGS); RNA-Seq; Ribo-Seq; VAR-Seq.

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Figures

Fig. 1
Fig. 1
Workflow steps with input/output file operations are controlled by SYSargs objects. Each SYSargs instance is constructed from a targets and a param file. The only input required from the user is the initial targets file. Subsequent instances are created automatically. Any number of predefined or custom workflow steps is supported
Fig. 2
Fig. 2
Workflow Steps and Graphical Features. Relevant workflow steps of several NGS applications (a) are illustrated in form of a simplified flowchart (b). Examples of systemPipeR’s functionalities are given under (c) including: (1) eight different plots for summarizing the quality and diversity of short reads provided as FASTQ files; (2) strand-specific read count summaries for all feature types provided by a genome annotation; (3) summary plots of read depth coverage for any number of transcripts with nucleotide resolution upstream/downstream of their start and stop codons, as well as binned coverage for their coding regions; (4) enumeration of up- and down-regulated DEGs for user defined sample comparisons; (5) similarity clustering of sample profiles; (6) 2-5-way Venn diagrams for DEGs, peak and variant sets; (7) gene-wise clustering with a wide range of algorithms; and (8) support for plotting read pileups and variants in the context of genome annotations along with genome browser support
See this image and copyright information in PMC

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