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
|
|
Submitter | This 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 |