A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by the Centre for Infectious Disease Genomics and One Health (CIDGOH), at Simon Fraser University, is now an open-source collaboration with contributions…

A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 or Mpox genomes. Workflow is developed in collaboration with VIRUS-MVP (https://github.com/cidgoh/VIRUS-MVP) which can be used to visualize the mutation profiles and functional annotations.

VirusMVP is an interactive heatmap-centric app that integrates viral genomic mutations, lineage information and curated functional impact to study the spread and evolution of viruses in Canada and globally.

Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data

This is the DataHarmonizer spreadsheet web application bundled with pathogen genomics data entry and validation templates

A data specification for harmonizing One Health AMR pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a spreadsheet collection template, supported by field and reference guides as well as different curation and new term request SOPs.

A data specification for harmonizing Wastewater pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via metadata template(s), supported by field and reference guides as well as different curation and new term request SOPs.

A One Health data specification harmonizing gold-standard microbial AMR datasets, developed under JPIAMR’s B2B2B AMRDx project. The specification provides standardized ontology-based fields and terms, implemented via the DataHarmonizer tool and supported by detailed reference guides and a new term request SOP.

This tool is designed to track and log versions and details of bioinformatics databases. It provides a streamlined way to monitor changes, with results stored in an SQLite database or directly added to a Google Sheet for easy sharing and collaboration.

A data specification for harmonizing MPox pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a the DataHarmonizer, supported by field and reference guides as well as different curation and new term request SOPs.