cidgoh Goto Github PK

aiv_seeker

AIV_seeker is optimized for detecting and identification of Avian Influenza Virus from metagenomics data.

aws-irida-deployment

cc_data_manager

cidgoh.github.io

cidgoh_ip_monitor

cidgoh_qc

Workflow for quality check for NGS data

covidmvp_deployment

Deployment of covid map app using docker

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.

datatype_mapper

An application that provides a suite of field datatype parsing and mapping expressions. It aims to achieve bi-directional data exchange.

fastauploader

A tool for batch processing large fasta files and accompanying metadata table to upload to repositories via API

ffp_phylogeny

A Galaxy tool for calculating Feature Frequency Profiles (FFP) from fasta sequence and text data.

geem

Genomic Epidemiology Entity Mart

grdi_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.

lexmapr

LexMapr: A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms

miso_lims_cloud

nf-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.

nf-seqqc

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

nf-upcoastv

ontotraining

A repository for ontology training materials

ontotrek

A 3d ontology visualizer focusing on OBOFoundry.org ontologies

pathogen-genomics-package

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

pathogen-mutation-functionalannotation-package

Package for functional annotation of mutations

rcqc

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.

snakemake_demo

specification-training

Training materials about developing and applying data specifications

training

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.

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.