Accession PRJCA004509
Title FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science
Relevance Medical
Data types Genome sequencing and assembly
Organisms Severe acute respiratory syndrome coronavirus 2
Description 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 collecton of a previouslly 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.
Sample scope Multispecies
Release date 2021-03-02
Publication
PubMed ID Article title Journal name DOI Year
31346170
Grants
Agency program Grant ID Grant title
Office of Counterterrorism and Emerging Threats, Food and Drug Administration, Department of Health and Human Services HHSF223201310109C
Office of Counterterrorism and Emerging Threats, Food and Drug Administration, Department of Health and Human Services HHSF223201510106C
Office of Counterterrorism and Emerging Threats, Food and Drug Administration, Department of Health and Human Services HHSF223201610073C
Department of Defense 224-15-6506R
DTRA CB10245
Food and Drug Administration TBD
Accessions in other database
Accession Database name
PRJNA231221 NCBI
SubmitterThis record was originated from NCBI and submitted by NGDC.
Organization US Food and Drug Administration; University of Maryland School of Medicine Institute for Genome Sciences (IGS) - sequencing center
Submission date 2021-02-19

Project Data

Resource name Description
BioSample (1) -
SAMC343820 Pathogen: clinical or host-associated sample from Severe acute respiratory syndrome coronavirus 2