Database for Reference Grade Microbial Sequences

The FDA ARGOS database generates and publishes quality-controlled microbial reference genomes for diagnostic use, which enable ID-NGS developers to perform in silico validation of their workflows. FDA partnered with IGS in 2013 to provide microbial genome sequencing, analysis, and deposition to public databases in support of the ARGOS database.

Contributing Genomes to FDA-ARGOS:

Further population and curation of the database will support the success of FDA-ARGOS and promote adoption by the NGS community. The FDA-ARGOS team openly invites additional collaborators from the scientific community to assist in filling the gaps in this public resource. The FDA-ARGOS and collaborators are specifically searching for unique, hard to source microbes such as biothreat organisms, emerging pathogens, and clinically significant bacterial, viral, fungal, and parasitic genomes. The goal is to collect sequence information for a minimum of 5 isolates per species. These isolates will be sequenced using a combination of long-read and short-read technologies, assembled, annotated, and made publicly available.

If you would like to contribute samples to FDA ARGOS for free sequencing and analysis, please review the sample submission guidelines, and submit a submission request.

For questions about the database or application process, please contact the ARGOS team or the IGS Genomics Resource Center.


Many infectious diseases have similar signs and symptoms, making it challenging for healthcare providers to identify the disease-causing agent. Clinical samples are often tested by multiple test methods to help reveal the particular microbe that is causing the infectious disease. The results of these test methods can help healthcare professionals determine the best treatment for patients. Today, High-Throughput Sequencing (HTS) or Next Generation Sequencing (NGS) technology has the capability, as a single test, to accomplish what might have required several different tests in the past.

NGS technology may allow the diagnosis of infections without prior knowledge of disease(s) cause. NGS technology can potentially reveal the presence of all microorganisms in a patient sample. Using infectious disease NGS (ID-NGS) technology, each microbial pathogen may be identified by its unique genomic fingerprint. The vision of ID-NGS technology is to further improve patient care by delivering diagnostics which can help identify the microbial makeup in patient samples quickly and accurately.

A new and flexible regulatory strategy is being developed to evaluate ID-NGS diagnostic devices to help promote innovation, combat global threats and advance public health. To support this mission, FDA, in collaboration with the Department of Defense (DoD), the Institute for Genome Sciences at the University of Maryland and the National Center for Biotechnology Information (NCBI), established a public microbial reference database (FDA-ARGOS) that contains quality controlled and curated genomic sequence data to support research and regulatory decisions. This evolving database could be used as a tool for in-silico (computer simulation) performance validation. Use of FDA-ARGOS genomes for in-silico data analysis can potentially reduce the testing burden on industry for ID-NGS devices.