title: aRNApipe: a balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments.
abstract: CONCLUSIONS
  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.
  https://github.com/HudsonAlpha/aRNAPipe ; DOI: 10.5281/zenodo.202950.
  
  
  BACKGROUND
  rmyers@hudsonalpha.org.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.|Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain.
authors.forename: Arnald
authors.initials: A
authors.lastname: Alonso
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
authors.forename: Brittany N
authors.initials: BN
authors.lastname: Lasseigne
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
authors.forename: Kelly
authors.initials: K
authors.lastname: Williams
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
authors.forename: Josh
authors.initials: J
authors.lastname: Nielsen
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.|Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL, USA.
authors.forename: Ryne C
authors.initials: RC
authors.lastname: Ramaker
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.|Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL, USA.
authors.forename: Andrew A
authors.initials: AA
authors.lastname: Hardigan
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
authors.forename: Bobbi
authors.initials: B
authors.lastname: Johnston
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
authors.forename: Brian S
authors.initials: BS
authors.lastname: Roberts
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
authors.forename: Sara J
authors.initials: SJ
authors.lastname: Cooper
authors.affiliation: Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain.
authors.forename: Sara
authors.initials: S
authors.lastname: Marsal
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
authors.forename: Richard M
authors.initials: RM
authors.lastname: Myers
mesh_terms: D017398:Alternative Splicing; D003205:Computing Methodologies; D060005:Genotyping Techniques / Q000379:methods; D006801:Humans; D012313:RNA / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D057188:Workflow
chemical_list: D012313:RNA