title: SePIA: RNA and small RNA sequence processing, integration, and analysis.
abstract: BACKGROUND
  Large-scale sequencing experiments are complex and require a wide spectrum of computational tools to extract and interpret relevant biological information. This is especially true in projects where individual processing and integrated analysis of both small RNA and complementary RNA data is needed. Such studies would benefit from a computational workflow that is easy to implement and standardizes the processing and analysis of both sequenced data types.
  
  
  RESULTS
  We developed SePIA (Sequence Processing, Integration, and Analysis), a comprehensive small RNA and RNA workflow. It provides ready execution for over 20 commonly known RNA-seq tools on top of an established workflow engine and provides dynamic pipeline architecture to manage, individually analyze, and integrate both small RNA and RNA data. Implementation with Docker makes SePIA portable and easy to run. We demonstrate the workflow's extensive utility with two case studies involving three breast cancer datasets. SePIA is straightforward to configure and organizes results into a perusable HTML report. Furthermore, the underlying pipeline engine supports computational resource management for optimal performance.
  
  
  CONCLUSIONS
  SePIA is an open-source workflow introducing standardized processing and analysis of RNA and small RNA data. SePIA's modular design enables robust customization to a given experiment while maintaining overall workflow structure. It is available at http://anduril.org/sepia.
authors.affiliation: Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland.
authors.forename: Katherine
authors.initials: K
authors.lastname: Icay
authors.affiliation: Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland.
authors.forename: Ping
authors.initials: P
authors.lastname: Chen
authors.affiliation: Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland.
authors.forename: Alejandra
authors.initials: A
authors.lastname: Cervera
authors.affiliation: Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland.
authors.forename: Ville
authors.initials: V
authors.lastname: Rantanen
authors.affiliation: Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland.
authors.forename: Rainer
authors.initials: R
authors.lastname: Lehtonen
authors.affiliation: Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland.
authors.forename: Sampsa
authors.initials: S
authors.lastname: Hautaniemi
keywords: Breast cancer; Integration; RNA; Sequencing; miRNA; totalRNA