Epiviz File Server: Query, transform and interactively explore data from indexed genomic files

Abstract

Motivation: Genomic data repositories like The Cancer Genome Atlas, Encyclopedia of DNA Elements, Bioconductor's AnnotationHub and ExperimentHub etc., provide public access to large amounts of genomic data as flat files. Researchers often download a subset of data files from these repositories to perform exploratory data analysis. We developed Epiviz File Server, a Python library that implements an in situ data query system for local or remotely hosted indexed genomic files, not only for visualization but also data transformation. The File Server library decouples data retrieval and transformation from specific visualization and analysis tools and provides an abstract interface to define computations independent of the location, format or structure of the file. We demonstrate the File Server in two use cases: (i) integration with Galaxy workflows and (ii) using Epiviz to create a custom genome browser from the Epigenome Roadmap dataset.

Availability and implementation: Epiviz File Server is open source and is available on GitHub at http://github.com/epiviz/epivizFileServer. The documentation for the File Server library is available at http://epivizfileserver.rtfd.io.