New Bioinformatic Platform Seeks to Democratize Genomics

November 30, 2016
New Bioinformatic Platform Seeks to Democratize Genomics
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Researchers at Los Alamos National Laboratory and their collaborators at the Naval Medical Research Center have developed a new bioinformatics platform they believe will help democratize the genomics revolution, by allowing users with limited bioinformatics expertise to analyze and interpret genomic sequence data quickly. Findings about the new platform—named Empowering the Development of Genomics Expertise (EDGE)—were published recently in Nucleic Acids Research through an article entitled “Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform.”

“We realized that while next-generation sequencing instruments are becoming more widespread and more accessible to the average biologist or physician, the bioinformatics tools required to process and analyze the data were not as user-friendly or accessible," said Patrick Chain, Ph.D., scientist of Los Alamos' biosecurity and public health group and EDGE team lead. "Given the large number of applications where sequencing is now used, a robust bioinformatics platform that encapsulates a broad array of algorithms is required to help address questions a researcher may have. We sought to develop a web-based environment where non-bioinformatics experts could easily select what pipelines they need and rapidly obtain results and interact with their data."

The ability to characterize organisms through accurately and rapidly comparing genomic data is an important part of Los Alamos' national security mission. As stopping the spread of disease—from naturally occurring or manmade threats—requires an in-depth understanding of pathogens and how they work.

Advancements in technology have fueled the development of new sequencing applications and will flood current databases with raw data. Several factors limit the use of these data currently, including a large number of associated software and hardware dependencies and the detailed expertise required to perform this analysis. To address these issues, Dr. Chain and his team developed an intuitive, web-based environment with a wide assortment of integrated and pioneering bioinformatics tools in preconfigured workflows, all of which can be readily applied to isolate genome sequencing or metagenomics projects.

EDGE is a user-friendly and open-source platform that integrates hundreds of cutting-edge tools and helps reduce data analysis times, from days or weeks to minutes or hours. The workflows in EDGE, along with its ease of use, provide novice next-generation sequencing users with the ability to perform many sophisticated analyses with only a few mouse clicks. This bioinformatics platform is described as an initial attempt at empowering the development of genomics expertise, as its name suggests, for a broad range of applications in microbial research.