Empowering the Development of Genomics Expertise (EDGE): Making Genomics Accessible to Everyone

Casandra Philipson34 ,Chien-Chi Lo1, Po-E Li1, Logan Voegtly23, Joseph J. Anderson23, Kimberly A. Bishop-Lilly23, Pavel Senin1, Yan Xu1, Karen Davenport1, Theron Hamilton3, Patrick Chain11 Los Alamos National Laboratory 2... [ view full abstract ]

Casandra Philipson³⁴ ,Chien-Chi Lo¹, Po-E Li¹, Logan Voegtly²³, Joseph J. Anderson²³, Kimberly A. Bishop-Lilly²³, Pavel Senin¹, Yan Xu¹, Karen Davenport¹, Theron Hamilton³, Patrick Chain¹

1 Los Alamos National Laboratory

2 Henry M. Jackson Foundation

3 Naval Medical Research Center, Biological Defense Research Directorate

4 Defense Threat Reduction Agency

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the ease of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research. EDGE is under constant development to expand its capabilities. The latest version of EDGE, version 1.5, includes several new features:

• Identification of AMR and virulence genes
• 16S/18S/fungal ITS analysis using QIIME:
• Integration of metadata collection/storage
• Comparison of multiple metagenomics samples’ taxonomy results

EDGE is under active development to version 2.0, which is expected to be released by 2018 and will include the following new modules:

• Pathogen analysis and characterization
• Differential gene expression (RNA-Seq)
• Presence/absence of targeted amplicons

EDGE version 1.1 Demo website: https://bioedge.lanl.gov

Nucleic Acids Research Article: https://doi.org/10.1093/nar/gk...