Background

EDGE bioinformatics was developed to help biologists rapidly process next-generation sequencing (NGS) data even if they have little to no bioinformatics expertise. EDGE is a highly integrated and interactive web-based platform that is capable of running many of the standard analyses that biologists require for viral, bacterial/archaeal, and metagenomic samples. EDGE provides an intuitive web-based interface for user input, allows users to visualize and interact with selected results, and generates a final detailed PDF report. Results in the form of tables, text files, graphic files, and PDFs, together with the raw output files of executed programs, can all be downloaded. A user management system allows tracking of an individual’s EDGE runs, along with the ability to share, post publicly, delete, or archive their results. Users can explore ongoing data processing within a user-friendly, intuitive web-based environment and interactive results are presented on a sample-by-sample basis. While EDGE was intentionally designed to be as simple as possible for the user, there is still no single ‘tool’ or algorithm that fits all use cases in the bioinformatics field. Our intent is to provide a detailed panoramic view of the user’s sample from various analytical standpoints. The initial release of EDGE in January 2017 provides six analytical workflows: pre-processing (data QC and host removal), assembly and annotation, reference-based analysis, taxonomy classification, phylogenetic analysis, and PCR analysis (validation and design). The latest release (version 1.5) includes several new features: identification of antimicrobial resistance and virulence genes, 16S/18S/fungal ITS analysis using QIIME, metadata collection/storage, and comparative analysis of taxonomic classification of multiple metagenomic samples. EDGE Bioinformatics is an ongoing effort to provide best of breed bioinformatics tools for NGS data analysis. Updates to current modules are continuous and more modules are under development.