RT Journal Article
SR Electronic
T1 aRNApipe: A balanced, efficient and distributed pipeline for processing RNA-seq data in high performance computing environments
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 060277
DO 10.1101/060277
A1 Arnald Alonso
A1 Brittany N. Lasseigne
A1 Kelly Williams
A1 Josh Nielsen
A1 Ryne C. Ramaker
A1 Andrew A Hardigan
A1 Bobbi Johnston
A1 Brian S. Roberts
A1 Sara J. Cooper
A1 Sara Marsal
A1 Richard M. Myers
YR 2016
UL http://biorxiv.org/content/early/2016/06/22/060277.abstract
AB Summary 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, 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.Availability and documentation https://github.com/HudsonAlpha/aRNAPipeContact rmyers{at}hudsonalpha.orgSupplementary information Supplementary data are available.