EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure

Area of Science:

• Microbial genomics
• Bioinformatics
• Computational biology

Background:

• The EDGAR platform is a well-established web server for comparative genomics and phylogenomics, providing precomputed orthology data for microbial genomes.
• It enables identification of gene content like pan-genome, core-genome, and singletons, alongside visualizations such as Venn diagrams and phylogenetic trees.
• Recent growth in analyzed genomes necessitated a technical overhaul to maintain performance and expand capabilities.

Purpose of the Study:

• To introduce EDGAR 3.0, a redesigned platform addressing the challenges of analyzing massive genomic datasets.
• To detail the new technical backend infrastructure supporting enhanced computational efficiency and scalability.
• To highlight new analytical features and expanded public database access within the updated platform.

Main Methods:

• Implementation of a scalable Kubernetes cluster in a cloud environment for computational tasks.
• Development of a new file-based, high-performance storage backend for efficient data handling.
• Leveraging parallelization and memory-efficient calculations for ortholog identification and analysis.

Main Results:

• Drastically reduced processing times for comparative genomic analyses.
• Introduction of new features including POCP and FastANI genome similarity indices, UpSet plots, and circular genome plots.
• Expansion of the public database to include 24,317 genomes across 749 projects.

Conclusions:

• EDGAR 3.0 provides a robust, scalable infrastructure for comprehensive microbial comparative gene content analysis.
• The platform's enhanced capabilities facilitate deeper insights into microbial genome evolution and function.
• The updated web server is accessible at http://edgar3.computational.bio, offering free access to extensive genomic data and analysis tools.