FDA-ARGOS WIKI - Revision history

Christie.woodside at 19:36, 7 April 2026

2026-04-07T19:36:09Z

← Older revision		Revision as of 19:36, 7 April 2026
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	== Introduction ==
			<div style="clear:both;"></div>

			<!-- INTRODUCTION -->
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			<h2>Introduction</h2>

	FDA-ARGOS database updates may help researchers rapidly validate diagnostic tests and use qualified genetic sequences to support future product development. NCBI BioProject [https://www.ncbi.nlm.nih.gov/bioproject/231221 PRJNA231221]		FDA-ARGOS database updates may help researchers rapidly validate diagnostic tests and use qualified genetic sequences to support future product development. NCBI BioProject [https://www.ncbi.nlm.nih.gov/bioproject/231221 PRJNA231221]
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	As of September 2021, Embleema and George Washington University have been conducting bioinformatic research and system development, focusing on expanding the FDA-ARGOS database. This project expands datasets publicly available in FDA-ARGOS, improves quality control by developing quality matrix tools and scoring approaches that will allow the mining of public sequence databases, and identifies high-quality sequences for upload to the FDA-ARGOS database as regulatory-grade sequences. Building on expansions during the COVID-19 pandemic, this project aims to further improve the utility of the FDA-ARGOS database as a key tool for medical countermeasure development and validation.		As of September 2021, Embleema and George Washington University have been conducting bioinformatic research and system development, focusing on expanding the FDA-ARGOS database. This project expands datasets publicly available in FDA-ARGOS, improves quality control by developing quality matrix tools and scoring approaches that will allow the mining of public sequence databases, and identifies high-quality sequences for upload to the FDA-ARGOS database as regulatory-grade sequences. Building on expansions during the COVID-19 pandemic, this project aims to further improve the utility of the FDA-ARGOS database as a key tool for medical countermeasure development and validation.

	For additional details on project information and assembly QC see		For additional details on project information and assembly QC see:

	* [https://www.fda.gov/emergency-preparedness-and-response/preparedness-research/expanding-next-generation-sequencing-tools-support-pandemic-preparedness-and-response FDA-ARGOS Project Information from FDA Announcements]		* [https://www.fda.gov/emergency-preparedness-and-response/preparedness-research/expanding-next-generation-sequencing-tools-support-pandemic-preparedness-and-response FDA-ARGOS Project Information from FDA Announcements]
	* [https://data.argosdb.org/ ARGOS Database]		* [https://data.argosdb.org/ ARGOS Database]
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	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.		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.
			</div>

	== FDA-ARGOS Database ==		<!-- FDA-ARGOS DATABASE -->
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			<h2>FDA-ARGOS Database</h2>

	The FDA-ARGOS database ([https://data.argosdb.org/ data.argosdb.org]) is a public database containing quality-controlled reference genomes for diagnostic and regulatory purposes.		The FDA-ARGOS database ([https://data.argosdb.org/ data.argosdb.org]) is a public database containing quality-controlled reference genomes for diagnostic and regulatory purposes.


	The organisms in the database tables that have FDA-ARGOS tags can be found in our FDA-ARGOS NCBI BioProject [https://www.ncbi.nlm.nih.gov/bioproject/231221 here]. We also have QC'd and included additional organisms that were publicly available on NCBI. They are logged in this page, [[Additional ARGOS Reviewed Organisms]].		The organisms in the database tables that have FDA-ARGOS tags can be found in our FDA-ARGOS NCBI BioProject [https://www.ncbi.nlm.nih.gov/bioproject/231221 here]. We also have QC'd and included additional organisms that were publicly available on NCBI. They are logged in this page, [[Additional ARGOS Reviewed Organisms]].

	A comprehensive reference table of human pathogenic organisms, including bacteria, viruses, and eukaryotic pathogens, has been created. The table integrates data from multiple curated sources and includes taxonomic identifiers and classification information for downstream analysis and database integration.		A comprehensive reference table of human pathogenic organisms, including bacteria, viruses, and eukaryotic pathogens, has been created. The table integrates data from multiple curated sources and includes taxonomic identifiers and classification information for downstream analysis and database integration.

	* [[Comprehensive Pathogenic Organisms Reference]].		* [[Comprehensive Pathogenic Organisms Reference]]

			For a visual display of data analytics, view the prototype dashboard [https://studyanalytics.embleema.com/superset/dashboard/argos/?standalone=2&expand_filters=0 here]. This is a static webpage that will be updated with each push.
			</div>

			<!-- FDA-ARGOS FAQS -->
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			<h2>FDA-ARGOS FAQs</h2>

	~~For a visual display of data analytics, view the prototype dashboard~~ [~~https://studyanalytics.embleema.com/superset/dashboard/argos/?standalone=2&expand_filters=0~~ here]. ~~This is a static webpage that will be updated with each push~~.		Frequently asked questions about FDA-ARGOS can be found [[FDA-ARGOS FAQs\|here]]. If there are any further questions, feel free to [[ARGOS Contact Us\|contact us]].
			</div>

	~~== FDA~~-ARGOS ~~FAQs =~~=		<!-- ARGOS USAGE TUTORIALS AND PROTOCOLS -->
	~~Frequently asked questions about FDA~~-~~ARGOS can be found [[FDA-ARGOS FAQs\|here]]~~. ~~If there are any further questions, feel free to [[~~ARGOS ~~Contact Us\|contact us]].~~		<div style="margin:10px 0; border:1px solid #CCC; padding:0 12px 12px 12px; box-shadow:0 2px 2px rgba(0,0,0,0.1); background:#f5faff;">
			<h2>ARGOS Usage Tutorials and Protocols</h2>

	== ARGOS Usage ~~Tutorials and Protocols ==~~		The ARGOS One-Click Pipeline is used to create the QC metrics and results displayed in our data tables on data.argosdb.org. The ARGOS One-Click Pipeline Usage tutorial can be found [[ARGOSQC Usage Tutorial\|here]].
			</div>

	The ARGOS One-Click Pipeline is used to create the QC metrics and results displayed in our data tables on data.argosdb.org. The ARGOS One-Click Pipeline Usage tutorial can be found [[ARGOSQC Usage Tutorial\|here]].
	~~Resources:~~
	* [[ARGOSQC Usage Tutorial\|ARGOS One-Click Pipeline Usage Tutorial]]
	</div>		</div>

Christie.woodside at 19:33, 7 April 2026

2026-04-07T19:33:58Z

@@ Line 1: / Line 1: @@
 == Introduction ==
@@ Line 44: / Line 58: @@
 The ARGOS One-Click Pipeline is used to create the QC metrics and results displayed in our data tables on data.argosdb.org. The ARGOS One-Click Pipeline Usage tutorial can be found [[ARGOSQC Usage Tutorial|here]].
-== Project Publications ==
+Resources:
-*Sichtig, H., Minogue, T., Yan, Y. ''et al.'' FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science. ''Nat Commun'' 10, 3313 (2019). https://doi.org/10.1038/s41467-019-11306-6
+</div>

Christie.woodside: /* FDA-ARGOS Database */

2026-04-07T19:16:47Z

FDA-ARGOS Database

← Older revision		Revision as of 19:16, 7 April 2026
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	The organisms in the database tables that have FDA-ARGOS tags can be found in our FDA-ARGOS NCBI BioProject [https://www.ncbi.nlm.nih.gov/bioproject/231221 here]. We also have QC'd and included additional organisms that were publicly available on NCBI. They are logged in this page, [[Additional ARGOS Reviewed Organisms]].		The organisms in the database tables that have FDA-ARGOS tags can be found in our FDA-ARGOS NCBI BioProject [https://www.ncbi.nlm.nih.gov/bioproject/231221 here]. We also have QC'd and included additional organisms that were publicly available on NCBI. They are logged in this page, [[Additional ARGOS Reviewed Organisms]].

			A comprehensive reference table of human pathogenic organisms, including bacteria, viruses, and eukaryotic pathogens, has been created. The table integrates data from multiple curated sources and includes taxonomic identifiers and classification information for downstream analysis and database integration.

	* [[Comprehensive Pathogenic Organisms Reference]].		* [[Comprehensive Pathogenic Organisms Reference]].

Christie.woodside: /* FDA-ARGOS Database */

2026-04-07T19:15:39Z

FDA-ARGOS Database

← Older revision		Revision as of 19:15, 7 April 2026
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	The FDA-ARGOS database ([https://data.argosdb.org/ data.argosdb.org]) is a public database containing quality-controlled reference genomes for diagnostic and regulatory purposes.		The FDA-ARGOS database ([https://data.argosdb.org/ data.argosdb.org]) is a public database containing quality-controlled reference genomes for diagnostic and regulatory purposes.

	* FDA-ARGOS ~~NCBI BioProject~~ can be found [https://www.ncbi.nlm.nih.gov/bioproject/231221 here].
	* [[Additional ARGOS Reviewed Organisms]].		The organisms in the database tables that have FDA-ARGOS tags can be found in our FDA-ARGOS NCBI BioProject [https://www.ncbi.nlm.nih.gov/bioproject/231221 here]. We also have QC'd and included additional organisms that were publicly available on NCBI. They are logged in this page, [[Additional ARGOS Reviewed Organisms]].

	* [[Comprehensive Pathogenic Organisms Reference]].		* [[Comprehensive Pathogenic Organisms Reference]].

Miaowang: /* FDA-ARGOS Database */

2026-03-31T17:31:04Z

FDA-ARGOS Database

← Older revision		Revision as of 17:31, 31 March 2026
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	* FDA-ARGOS NCBI BioProject can be found [https://www.ncbi.nlm.nih.gov/bioproject/231221 here].		* FDA-ARGOS NCBI BioProject can be found [https://www.ncbi.nlm.nih.gov/bioproject/231221 here].
	* [[Additional ARGOS Reviewed Organisms]].		* [[Additional ARGOS Reviewed Organisms]].
	* [[Comprehensive Pathogenic Organisms Reference]]		* [[Comprehensive Pathogenic Organisms Reference]].

Miaowang at 16:33, 31 March 2026

2026-03-31T16:33:49Z

← Older revision		Revision as of 16:33, 31 March 2026
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	* FDA-ARGOS NCBI BioProject can be found [https://www.ncbi.nlm.nih.gov/bioproject/231221 here].		* FDA-ARGOS NCBI BioProject can be found [https://www.ncbi.nlm.nih.gov/bioproject/231221 here].
	* [[Additional ARGOS Reviewed Organisms]].		* [[Additional ARGOS Reviewed Organisms]].
			* [[Comprehensive Pathogenic Organisms Reference]]

Miaowang: /* FDA-ARGOS Database */

2026-03-31T14:45:22Z

FDA-ARGOS Database

← Older revision		Revision as of 14:45, 31 March 2026
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	* FDA-ARGOS NCBI BioProject can be found [https://www.ncbi.nlm.nih.gov/bioproject/231221 here].		* FDA-ARGOS NCBI BioProject can be found [https://www.ncbi.nlm.nih.gov/bioproject/231221 here].
	* [[Additional ARGOS Reviewed Organisms]].		* [[Additional ARGOS Reviewed Organisms]].
	* Comprehensive Human Pathogen List - Here is the comprehensive human pathogens list. The list includes 1,717 bacteria, 1,639 viruses, and 49 fungal/eukaryotic organisms.

Miaowang: /* FDA-ARGOS Database */

2026-03-27T00:00:27Z

FDA-ARGOS Database

← Older revision		Revision as of 00:00, 27 March 2026
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	* FDA-ARGOS NCBI BioProject can be found [https://www.ncbi.nlm.nih.gov/bioproject/231221 here].		* FDA-ARGOS NCBI BioProject can be found [https://www.ncbi.nlm.nih.gov/bioproject/231221 here].
	* [[Additional ARGOS Reviewed Organisms]].		* [[Additional ARGOS Reviewed Organisms]].
			* Comprehensive Human Pathogen List - Here is the comprehensive human pathogens list. The list includes 1,717 bacteria, 1,639 viruses, and 49 fungal/eukaryotic organisms.

Christie.woodside: /* Project Publications */

2025-09-08T17:19:14Z

Project Publications

← Older revision		Revision as of 17:19, 8 September 2025
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	== Project Publications ==		== Project Publications ==

	*Sichtig, H., Minogue, T., Yan, Y. ''et al.'' FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science. ''Nat Commun'' 10, 3313 (2019). https://doi.org/10.1038/s41467-019-11306-6<br />		*Sichtig, H., Minogue, T., Yan, Y. ''et al.'' FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science. ''Nat Commun'' 10, 3313 (2019). https://doi.org/10.1038/s41467-019-11306-6
			*Coming Soon: Journal Publication highlighting our QC metrics and data dictionary for the ARGOS Database<br />

Christie.woodside: /* FDA-ARGOS Database */

2025-09-08T17:15:58Z

FDA-ARGOS Database

← Older revision		Revision as of 17:15, 8 September 2025
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	For a visual display of data analytics, view the prototype dashboard [https://studyanalytics.embleema.com/superset/dashboard/argos/?standalone=2&expand_filters=0 here].		For a visual display of data analytics, view the prototype dashboard [https://studyanalytics.embleema.com/superset/dashboard/argos/?standalone=2&expand_filters=0 here]. This is a static webpage that will be updated with each push.

	== FDA-ARGOS FAQs ==		== FDA-ARGOS FAQs ==