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CRAMER: a lightweight, highly customizable web-based genome browser supporting multiple visualization instances.

M Anastasiadi1, E Bragin2, P Biojoux1

  • 1School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK.

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Summary

The Cranfield Genome Browser (CRAMER) enables easy creation of multiple, customizable genomic data visualization instances. This open-source tool streamlines the process for researchers needing personalized genome browsers.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Data Visualization

Background:

  • Genomic data generation has surged, increasing demand for personalized genome browsers.
  • Existing web-based genome browsers lack efficient methods for creating multiple, customized visualization instances without manual server setup.

Purpose of the Study:

  • To introduce the Cranfield Genome Browser (CRAMER), an open-source, customizable web application for interactive genomic data visualization.
  • To provide a solution for seamless creation and management of multiple, parallel visualization instances with user-controlled customization.

Main Methods:

  • CRAMER is a lightweight, Node.js deployed web application utilizing a MongoDB database for storing user customizations.
  • Supports visualization of diverse genomic data formats including annotation, variant calling, coverage, and gene expression.
  • Offers direct JavaScript coding for personalized tracks and supports track addition via file upload, remote links, or drag-and-drop functionality.

Main Results:

  • CRAMER facilitates the effortless deployment and parallel operation of multiple, independent genome visualization instances.
  • Users can extensively customize tracks both functionally and visually, enhancing data interpretation.
  • The browser efficiently handles various file formats and allows real-time data processing from remote sources.

Conclusions:

  • CRAMER offers a flexible and powerful solution for personalized genomic data visualization.
  • Its ability to create multiple instances and extensive customization options addresses limitations in current genome browsing tools.
  • The open-source nature and ease of deployment make CRAMER a valuable resource for the research community.