NCBI releases enhanced Pathogen Detection (Beta) Isolates Browser

NCBI has introduced a new and improved Pathogen DetectionBeta Isolates Browser. The browser is a key component of NCBI’s Pathogen Detection Project, a collaboration with FDA, CDC, USDA, and others to use whole genome sequencing data to monitor and investigate outbreaks of foodborne disease. Federal, state and other labs sequence pathogens (such as Salmonella and Listeria) isolated from patients, food, and environmental samples and submit the data in real time to NCBI. We then use our analysis pipeline to assemble the sequences and cluster them with all other isolates in the database to identify closely related sequences, thereby making it easier to identify cases that could be involved in an outbreak.

What’s new?

The browser is a completely updated interface that offers many improvements, like:

  • An enhanced search and browse interface
  • A new tree viewer that allows easy navigation of large SNP clusters

The NCBI Pathogen DetectionBeta home page allows direct access to sequence data, submission resources, and documentation.

How do I get started?

We suggest that you start from the NCBI Pathogen DetectionBeta home page (Figure 1).

pathogen detection beta homepage
Figure 1. Various ways to start accessing data from the Pathogen DetectionBeta home page.

Find isolates now!’ takes you directly to the isolates browser, where you can search for isolates, select an organism and start exploring. Another option is to use the organism-specific links in the table under ‘Explore the Data’. The ‘See more organisms’ link at the bottom of this table provides a full list of all organisms that we’re currently processing. Under “Data Resources”, you’ll find an FTP directory link if you’d like to download the data for your own analyses.

tree view of isolates
Figure 2. Viewing a closely related set of isolates.

How do I learn more?

One great way to dig deeper is to view our recent webinar on YouTube, which gives background information and covers the main features.

The NCBI Pathogen Detection Isolates Browser is currently in beta version and continuously evolving. We are working on adding new resistance genes for biocide, metal resistance, and virulence, and expect to introduce them in the near future. Further details can also be found in our product factsheet.

We invite you to explore the updated browser and send us your feedback, from the link provided on the browser, or  via email. We’d love to hear what you think!

2 thoughts on “NCBI releases enhanced Pathogen Detection (Beta) Isolates Browser

Leave a Reply