The Canadian Centre for Computational Genomics(C3G) leads and supports multiple large projects ranging from their development to deployment including software solutions, such as APIs and web applications, to facilitating the organization, discovery, visualization for both large-scale and small-scale projects. We have listed below the projects that we are involved in currently.

Genome Canada logo


As one of Genome Canada’s 10 Genomics Technology Platforms (GTP), C3G provides researchers across Canada and internationally with access to leading-edge bioinformatics software and for-fee services.


CoVSeq logo

CoVSeQ is a partnership between the Institut National de Santé Publique du Québec (INSPQ) , the McGill Genome Center and C3G to sequence the viral genomes of Quebec patients with COVID-19 disease. C3G is in charge of developing pipelines and analyzing the sequenced genomes

COVID-19 Resources Canada logo

C3G is a founding partner of COVID-19 Resources Canada, an online national platform to aggregate COVID-19 pandemic responses. This web community coordinates local volunteer initiatives, supports accelerated research and presents pandemic health issues in a trustworthy and accessible manner.

GenPipes logo

GenPipes was developed at the C3G as a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for High-Performance Computing clusters and the cloud. GenPipes comes with 12 validated and scalable pipelines for various genomics applications, including: RNA-seq, WGS, WES, ChIP-Seq, and HiC

Bento is an open-source genomic data sharing platform used to deploy data-focused portals. By adhering to existing and anticipated standards, APIs and schemas, such as from the Global Alliance for Genomics and Health (GA4GH), it facilitates interactions between various multi -omics research communities worldwide. Its reusable and interoperable components reduce the complexity and overhead of constructing data distribution portals. Many of our projects, such as the BQC19 and ICHANGE portals, rely on the Bento software infrastructure.

CanCOGEN logo

C3G supports data production and organization CGEn’s HostSeq project which aims to sequence genomes of 10,000 Canadians to help understand the genomic architecture of the host response to COVID-19.

Epishare logo

C3G drives the development of the EpiShare Open Science initiative to enhance the accessibility of epigenomic datasets and RNA expression reference data to users worldwide. In close collaboration with the International Human Epigenome Consortium (IHEC) and the Encyclopedia of DNA Elements (ENCODE), EpiShare adapts and extends GA4GH tools and standards to make accessing, sharing and analyzing epigenomic data more flexible.

Juno logo

Juno is a secure Infrastructure as a Service (IaaS) that allows researchers to store, access, share and analyze data at any scale, in a fully governed, highly secure environment, while maintaining control of their own data at all times. This project builds upon the successful HPC4Health secure cloud now used by researchers and clinicians at multiple Ontario hospitals. It is the product of a collaboration between C3G and Calcul Quebec.

Biobanque Quebecois COVID-19 logo

Mandated by Public Health Agency of Canada, the Fonds de recherche du Québec – Santé (FRQS) and Génome Québec in response to the COVID-19 pandemic, the BQC19 ensures that health scientists have access to the biological materials and data necessary for their COVID-19 research efforts. Their discoveries identify people most at risk and assist the government to prioritize health care system resources, prescribe social measures to control the spread of infection, plan the resumption of economic activities and to anticipate and better prepare for future pandemics. Its decentralized infrastructure allows the federation of provincial, national and international research.


EpiAtlas is a multi-institutional reprocessing initiative of the IHEC data. Using a containerized pipeline specifically designed for HPC environments, it yields a uniform, gold standard epigenomic atlas for many tissue types. The common processing methodology facilitates large-scale direct inter-tissue comparisons and alleviates the need for researchers to perform their own hardware intensive and time-consuming operations.

IHEC logo

The International Human Epigenome Consortium (IHEC) coordinates the production of reference epigenome maps. The IHEC Data Portal is the official source to navigate through IHEC’s >7,000 reference epigenomic datasets, generated from >600 tissues. The portal enhances the utility of these reference maps by facilitating the discovery, visualization, analysis, download, and sharing of epigenomics data through rich, intuitive interfaces.

Mi4 logo

McGill’s MI4 funds research on the role of microbes in human diseases and diseases for which there is a primary immunologic cause or for which the treatment is primarily directed at the immune system. C3G contributes to this initiative by supporting the microbiome research platform led by Dr Ken Dewar on all aspects of bioinformatics.

CanDIG logo
National scale analysis, but over locally-controlled data. C3G is a main contributor to CanDIG (Canadian Distributed Infrastructure for Genomics), a platform for the distributed analysis of locally-controlled and private genomic data. CanDIG builds upon established and in-progress projects such as OpenID Connect and Keycloak for authentication and the GA4GH (Global Alliance for Genomics and Health) APIs and schemas for genomic data and genomic data exchange.

The Genetics and Genomics Analysis Platform (GenAP) aims at facilitating the work of researchers and students by offering out of the box Web applications running on an infrastructure that currently leverages Compute Canada Cloud and HPC resources

Canadian SARS-CoV-2
Data Portal

The Canadian SARS-CoV-2 Data Portal that will manage and facilitate data sharing of viral genome sequences among Canadian public health labs, researchers and other groups interested in accessing the data for research and innovation purposes.

National Team

Compute Canada’s Bioinformatics National Team (BNT) is a partnership between Compute Canada, the BC Genome Sciences Centre and the C3G committed to a strategy that includes leveraging existing Compute Canada resources as well as developing new resources and practices.

McGill Genome Centre logo

The McGill Genome Centre provides Canadian and international researchers with high-throughput technologies and cutting-edge approaches to enable next-generation genomic studies. As its acting bioinformatics platform, C3G supports data production and technology development efforts of the MCG.