Funding period: 2023-2028
Lead: Adam Koziol and Catherine Carrillo
Total GRDI funding: $274,000
Regulatory food safety agencies aim to safeguard food supply with informed, risk-based approaches. Maximizing information from laboratory testing of inspection samples is crucial for effective responses. Genomics technologies, like next-generation sequencing (NGS), offer faster and more cost-effective comprehensive analyses. However, accessing and interpreting large genomic datasets pose challenges. To tackle this, the Ottawa Laboratory Carling team developed FoodPort, a user-friendly cloud application. This project aims to further enhance FoodPort on CFIA's Microsoft Azure cloud tenant, ensuring easy access and interpretation of food microbiology sequencing data for CFIA scientists. This effort is vital for efficient regulatory responses and ensuring food safety.
Research tool / process
PrimerFinder is software tool that was added as an enhancement to FoodPort to offer the following functionalities: 1) PrimerValidator, which evaluates binding of primer pairs against curated inclusivity/exclusivity panels; 2) PrimerVerifier, which evaluates binding of one or more primer pairs against flexible inclusivity/exclusivity panels; 3) PrimerFinder, which evaluates binding of one or more primer pairs against assemblies
AmpliSeq is a bioinformatics analysis pipeline used for amplicon sequencing, supporting denoising of any amplicon and supports a variety of taxonomic databases for taxonomic assignment. The FoodPort implementation of AmpliSeq allows users to upload sequencing reads, select primer sequences, read trimming and filtering options, taxonomy options, genus/genera to exlude, and the database, including the version of the database to use.
FileZone is a collection of tools on FoodPort that allow users to manage containers located in Azure cloud. There are three main functionalities of the FileZone: 1) Select an Existing Container, which allows users to specify a container name, and view, upload, or download files in the container; 2) Create a New Container, which allows users to create a new container, and upload files to the container; 3) Located files, which allows users to search for files and/or containers using regular expressions.
Dataset / database
Shiga Toxin Allele Database (StxDB): A comprehensive, curated database of Shiga toxins including all know nucleotide and protein sequence variants to enable accurate determination of Shiga-toxin variants. This database has now been curated to provide accession numbers for representative genomes to enable database users to assess reliability of results.
Contact us
Genomics R&D Initiative
Email: info@grdi-irdg.collaboration.gc.ca