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SRX9620855: Other Sequencing of Salmonella enterica
1 ILLUMINA (Illumina HiSeq 4000) run: 6.3M spots, 1.9G bases, 784.7Mb downloads

Design: gDNA was sheared to ~380 bp with a Covaris and prepared into an indexed, PE Illumina library
Submitted by: University of Maryland Institute for Genome Sciences (UMIGS)
Study: FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science
show Abstracthide Abstract
<b>FDA-ARGOS project update</b> FDA-ARGOS database updates may help researchers rapidly validate diagnostic tests and use qualified genetic sequences to support future product development 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 see <ul> <li> <a href="https://www.fda.gov/emergency-preparedness-and-response/mcm-regulatory-science/expanding-next-generation-sequencing-tools-support-pandemic-preparedness-and-response"> </a> </li> <li> <a href="https://data.argosdb.org/"<a> </li> </ul> <b>FDA-ARGOS Initial Phase</b> </li> </ul> In May 2014, the FDA and collaborators had 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 had initially collected and sequenced 2000 microbes that included biothreat microorganisms, common clinical pathogens, and closely related species. At the beginning of this project, the FDA-ARGOS microbial genomes were generated in 3 phases. Generally: <ul> <li>Phase 1 entailed collection of a previously identified microbe and nucleic acid extraction.</li> <li>Phase 2, the microbial nucleic acids were then sequenced and de novo assembled occurred 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 were then vetted by an ID-NGS subject matter expert working group that consisted of FDA personnel and collaborators and the data was then deposited in the 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.
Sample: BAA-1735D-5
SAMN16357413 • SRS7822863 • All experiments • All runs
Library:
Name: IL100132925
Instrument: Illumina HiSeq 4000
Strategy: WGS
Source: GENOMIC
Selection: RANDOM
Layout: PAIRED
Construction protocol: UMIGS-GRC Illumina Construction Protocol Details
Spot descriptor:
forward152  reverse

Runs: 1 run, 6.3M spots, 1.9G bases, 784.7Mb
Run# of Spots# of BasesSizePublished
SRR131830476,299,5101.9G784.7Mb2020-12-02

ID:
12570797

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