Bioinformatics Platform

“Our goal is to make sense of complexity—not just process data. We develop tailored pipelines that bring together genomic, transcriptomic, and proteomic information in ways that help researchers see the full picture.”

Hector Galvez & François Lefebvre

Genomic studies generate vast amounts of data that require sophisticated analytical approaches for meaningful interpretation. The Bioinformatics Platform at the McGill Genome Centre is powered by the Canadian Centre for Computational Genomics (C3G), a national bioinformatics infrastructure led by Dr. Guillaume Bourque. C3G provides standardized and custom pipelines for variant calling, transcriptomics, epigenomics, metagenomics, cancer genomics, and multi-omic integration.

Since 2011, C3G has supported over 1,300 analysis projects for more than 700 research groups across Canada and internationally. These services are powered by high-performance computing resources, including Abacus, the McGill Genome Centre’s dedicated cluster managed by Genome Centre IT, as well as infrastructure provided through SD4H and the Calcul Québec–Alliance network. This integrated environment supports the analysis of large and complex datasets by providing scalable computing power, secure storage, and robust data management tools. Together, these resources enable our team to deliver reproducible, interpretable insights that advance both basic and clinical research.

Common Applications

  • Variant calling, quality control, and annotation for disease gene discovery, population genetics, and evolutionary studies

  • Transcriptomics profiling, differential expression analysis, variant and gene fusion detection

  • Integrated somatic/germline variant pipelines with interactive reports for clinical and translational cancer research

  • Peak calling and multi-omics integration for epigenomic studies and regulatory element mapping

  • From amplicon or shotgun sequencing, microbial community profiling and related statistical analyses and visualizations

Canadian Centre for Computational Genomics (C3G) at the McGill Genome Centre in Montreal, Quebec

Technologies and Tools at the McGill Genome Centre

  • GenPipes from C3G at the McGill Genome Centre in Montreal, Quebec

    GenPipes

    Modular, open-source workflow management system developed in-house for high-throughput data processing (WGS, RNA-Seq, ChIP-Seq, etc.)

    GenPipes
  • Secure Data 4HHealth from C3G at the McGill Genome Centre in Montreal, Quebec

    Secure Data for Health (SD4H)

    Quebec-based secure cloud infrastructure for privacy-compliant health and genomics data analysis

    SD4H
  • BENTO from C3G at the McGill Genome Centre in Montreal, Quebec

    Bento

    Web-based platform for sharing and querying clinical and -omics data across large cohorts

    Bento

Platform deliverables

The deliverables provided by C3G vary by project. For custom data analyses, our analysts typically provide a summary report (in HTML or a similar format) detailing the methods used, the main results, and their expert interpretation in the context of the technology used and experimental objectives. Importantly, our team remains available for meetings throughout the project and will assist later stages, such as preparing data for submission to public repositories (e.g., GEO) and for publication. Large data files, such as CRAM files, are transferred via Globus, SFTP, or other secure methods, while data tracks for interactive exploration are hosted on our SD4H infrastructure.