Note: if you use
systemPipeR in published research, please cite:
Backman, T.W.H and Girke, T. (2016).
systemPipeR: NGS Workflow and Report Generation Environment. BMC Bioinformatics, 17: 388. 10.1186/s12859-016-1241-0.
systemPipeR provides flexible utilities for building and running automated end-to-end analysis workflows for a wide range of research applications, including next-generation sequencing (NGS) experiments, such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq (H Backman and Girke 2016). Important features include a uniform workflow interface across different data analysis applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters (Figure 1). The latter supports interactive job submissions and batch submissions to queuing systems of clusters. For instance,
systemPipeR can be used with most command-line aligners such as
BWA (Li 2013; Li and Durbin 2009),
HISAT2 (Kim, Langmead, and Salzberg 2015),
TopHat2 (Kim et al. 2013) and
Bowtie2 (Langmead and Salzberg 2012), as well as the R-based NGS aligners
Rsubread (Liao, Smyth, and Shi 2013) and
gsnap (gmapR) (Wu and Nacu 2010). Efficient handling of complex sample sets (e.g. FASTQ/BAM files) and experimental designs are facilitated by a well-defined sample annotation infrastructure which improves reproducibility and user-friendliness of many typical analysis workflows in the NGS area (Lawrence et al. 2013).
The main motivation and advantages of using
systemPipeR for complex data analysis tasks are: