PATH-SAFE powered by Pathogenwatch
Last updated
Last updated
Enhanced security: Separate logins, separate locked-down data storage on . PATH-SAFE Powered by Pathogenwatch sits behind 2-factor Authentication using CLIMB's Bryn interface. All PATH-SAFE data in Pathogenwatch is private and is only accessible to authorised PATH-SAFE users. Login credentials must be granted by CLIMB with approval from food safety agencies.
Standardised genome assembly pipeline - The genomic data displayed in Pathogenwatch for PATH-SAFE is assembled using Etoki. More details on the Etoki pipeline can be found .
Specialised genome analysis modules - genome analytics specific to food borne pathogens.
based on multiple genomes - users can start with a set of genomes (e.g. a saved search of genomes recently uploaded by their agency) and find other genomes that are genetically similar (e.g. genomes from other agencies or different timeframes).
Automatic folder management - no need for folder management page in the application
External uploads/submissions - no need for the upload page within the application
Preconfigured Saved Searches based on upload dates - easy visibility into recent work, facilitating new discoveries
Folders organise genomes submitted by different agencies. For PATH-SAFE, Folders are managed by the CLIMB and CGPS/DES teams, and genomes are placed in folders based on who uploaded them into the CLIMB portal. Searches are dynamic query results from Folders; they display a pre-specified moving window (subset) of the genomes added to those Folders. Collections are static, user-created investigations into what's shown in Searches, pulling in other genomes from the platform that are contextually similar. Collections are where users can customise their displays (e.g. custom colours, new trees, etc.).
PATH-SAFE genomes will be added to Pathogenwatch via the CLIMB platform by each agency's sequencing labs. PATH-SAFE Genomes cannot be uploaded directly to the Pathogenwatch site, so the Upload page has been disabled. The specifications for the sequence read & metadata files, including the required metadata formats, can be found on the , along with .
Genomes will be submitted as sequencing reads with associated metadata files, which will then be before being available on the Pathogenwatch interface.
Note that there are very few required metadata columns, and a limited number of optional columns. Additional columns are not allowed, in order to ensure that only shareable data are uploaded; this limitation addresses privacy concerns among agencies and their partner organisations.
PATH-SAFE submitters who have questions or would like assistance automating the formatting of their metadata should email path-safe@cgps.group
It is possible to edit metadata after uploading it, by using an endpoint provided by CLIMB. For help with this, please email path-safe@cgps.group
The PATH-SAFE program has a User Access Agreement to ensure security and enhance collaboration. If you are unsure about sharing and permissions, please contact your agency's PATH-SAFE administrator or team lead.