EDGAR 3.5: Advancing comparative genomics with new tools for microbial genome analysis

Introduction

The significant increase of whole genome sequence data availability, made possible by next generation sequencing methods, has caused the emergence of a variety of tools for the comparative analysis of related genomes. The web-based, EDGAR platform, is one of the most established tools, to highlight similarities and differences, conserved and divergent regions within microbial sequence data. EDGAR is being constantly updated for the last 15 years to serve the emerging needs of the scientific community. This work focuses on the latest developments on the EDGAR platform and expands on upcoming changes.

Objective

Since its inception, the average number of genomes analyzed per EDGAR project has steadily increased, as has the variety of methods employed by its community. As a consequence, the development of EDGAR pursues two main goals: First, to create the necessary infrastructure to accommodate the mounting data volumes. Second, to constantly improve the EDGAR website with new ways for scientists to examine their genomes.

Methods

We iterated further on our recently released functional category features and will soon offer the interactive exploration of KEGG subcategories organized in a sunburst plot. The GO term categorization has received a major upgrade, with it now being possible to calculate an enrichment analysis between a chosen subset of genomes. This is being additionally expanded upon in the form of a GO-Net visualization, which will make it possible to browse through the web of correlated genes and hierarchical GO-terms. Furthermore, we are working on a feature that enables our users to find, save, visualize and compare conserved syntenic gene clusters. The core ortholog calculation has been rewritten, making it faster by a factor of 50x, enabling EDGAR to scale into the ultra-high-throughput era. This will allow us to use binned subsets of the BakRep project to provide a significantly scaled-up version of EDGAR's public database in the near future.

Results

EDGAR continues to grow its capabilities, offering an increasingly diverse array of analysis methods for comparative genomics and phylogenomics in a single software framework. Our infrastructure and web platform offer researchers a time-effective way to gain various perspectives on their microbial genomes. For unpublished data, EDGAR offers private, password protected projects. Our web server is accessible at: https://edgar3.computational.bio