Database for Reference Grade Microbial Sequences (FDA-ARGOS)

In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA's Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.