systemPipeR

July 22, 2015

Outline

  • Introduction
  • Motivation
  • Design
  • Templates
  • Getting started

Introduction

  • systemPipeR is an R package for building end-to-end analysis pipelines with automated report generation for next generation NGS applications (Girke 2014).
  • Important features:
    • Support for R and command-line software, such as NGS aligners, peak callers, variant callers, etc.
    • Runs on single machines and compute clusters with schedulers
    • Uniform sample handling and annotation

Outline

  • Introduction
  • Motivation
  • Design
  • Templates
  • Getting started

Motivation

  • Many NGS applications share several analysis routines, such as:
    • Read QC and preprocessing
    • Alignments
    • Quantification
    • Feature annotations
    • Enrichment analysis
  • Thus, a common workflow environment has many advantages for improving efficiency, standardization and reproducibility

Advantages of systemPipeR

  • Facilitates design of complex NGS workflows involving multiple R/Bioconductor packages (Huber et al. 2015).
  • Makes NGS analysis with Bioconductor utilities more accessible to new users
  • Simplifies usage of command-line software from within R
  • Reduces complexity of using compute clusters for R and command-line software
  • Accelerates runtime of workflows via parallelization on computer systems with mutiple CPU cores and/or multiple compute nodes
  • Automates generation of analysis reports to improve reproducibility

Outline

  • Introduction
  • Motivation
  • Design
  • Templates
  • Getting started

Workflow design in systemPipeR

Drawing