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DataHarmonizer
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 from the National Microbiome Data Collaborative (NMDC), the LinkML development team, and others.LexMapr
LexMapr: A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology TermsGRDI_AMR_One_Health
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.pathogen-genomics-package
This is the DataHarmonizer spreadsheet web application bundled with pathogen genomics data entry and validation templatesnf-ncov-voc
A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.VIRUS-MVP
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.bacpaq
Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing datageem
Genomic Epidemiology Entity Martontotraining
A repository for ontology training materialsffp_phylogeny
A Galaxy tool for calculating Feature Frequency Profiles (FFP) from fasta sequence and text data.Wastewater_Contextual_Data_Specification
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.specification-training
Training materials about developing and applying data specificationsAWS-IRIDA-DEPLOYMENT
nf-upcoastv
FastaUploader
A tool for batch processing large fasta files and accompanying metadata table to upload to repositories via APIrcqc
Report Calc for Quality Control is a python command line and Galaxy bioinformatics platform tool for text-mining log and data files to create reports and even to stop workflow execution in response to critical quality control issues.Love Open Source and this site? Check out how you can help us