U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX2106985: Other Sequencing of Pasteurella multocida
1 ILLUMINA (Illumina HiSeq 2500) run: 1M spots, 211.7M bases, 132.5Mb 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
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: <ul> <li>Phase 1 entails collection of a previously identified microbe and nucleic acid extraction.</li> <li>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).</li> <li>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.</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: clinical isolate
SAMN04875587 • SRS1666263 • All experiments • All runs
Library:
Name: IL100056683
Instrument: Illumina HiSeq 2500
Strategy: WGS
Source: GENOMIC
Selection: RANDOM
Layout: PAIRED
Construction protocol: UMIGS-GRC Illumina Construction Protocol Details
Spot descriptor:
forward102  reverse

Runs: 1 run, 1M spots, 211.7M bases, 132.5Mb
Run# of Spots# of BasesSizePublished
SRR41249891,047,822211.7M132.5Mb2016-09-02

ID:
3101765

Supplemental Content

Search details

See more...

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...