SRA

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: <ul> <li>Phase 1 entails collection of a previously identified microbe and nucleic acid extraction.</li> <li>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).</li> <li>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.</li> </ul> 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.