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

Author:
Alonso, Arnald, Lasseigne, Brittany N., Williams, Kelly, Nielsen, Josh, Ramaker, Ryne C., Hardigan, Andrew A., Johnston, Bobbi, Roberts, Brian S., Cooper, Sara J., Marsal, Sara, Myers, Richard M.
Source:
Bioinformatics 2017 v.33 no.11 pp. 1727-1729
ISSN:
1460-2059
Subject:
alternative splicing, bioinformatics, genome assembly, messenger RNA, quality control
Abstract:
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, 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. Availability and documentation: https://github.com/HudsonAlpha/aRNAPipe; DOI: 10.5281/zenodo.202950 Contact: rmyers@hudsonalpha.org Supplementary information: Supplementary data are available at Bioinformatics online.
Agid:
6248570