ARNApipe: A balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments

Academic Article


  • The wide range of RNA-seq applications and their high-computational needs require the development of pipelines orchestrating the entire workflow and optimizing usage of available computational resources. We present aRNApipe, a project-oriented pipeline for processing of RNA-seq data in high-performance cluster environments. aRNApipe is highly modular and can be easily migrated to any high-performance computing (HPC) environment. The current applications included in aRNApipe combine the essential RNA-seq primary analyses, including quality control metrics, transcript alignment, count generation, transcript fusion identification, alternative splicing and sequence variant calling. aRNApipe is project-oriented and dynamic so users can easily update analyses to include or exclude samples or enable additional processing modules. Workflow parameters are easily set using a single configuration file that provides centralized tracking of all analytical processes. Finally, aRNApipe incorporates interactive web reports for sample tracking and a tool for managing the genome assemblies available to perform an analysis.
  • Published In

  • Bioinformatics  Journal
  • Digital Object Identifier (doi)

    Author List

  • Alonso A; Lasseigne BN; Williams K; Nielsen J; Ramaker RC; Hardigan AA; Johnston B; Roberts BS; Cooper SJ; Marsal S
  • Start Page

  • 1727
  • End Page

  • 1729
  • Volume

  • 33
  • Issue

  • 11