OICR Genome Sequence Informatics documentation

GSI is a team of bioinformaticians and software developers at Ontario Institute for Cancer Research that develop, maintain, and operate the core analysis infrastructure, analyze genomic data produced at the institute, and support collaborators and researchers with their bioinformatics analysis. To support these activities, we have developed a large suite of open-source software that can be found under our Github organizations: oicr-gsi and miso-lims.

Contact us

Contact us through the Github issue tracker on any project.

Accredited Pipelines

• Informatics Overview
• Updates and Upgrades
• Variables and Observations to Record
• Assays

Data Review and Reporting

• Overview of Clinical Reporting
• Before Starting
• Set up a Djerba working directory
• Generate and Interpret the Report
• Review the Draft Report
• Generate QC Report
• Upload to the Requisition System
• Revise a Draft Report
• Amended Reports
• Failed Reports
• Additional Considerations
• Reporting Tips

Research Use Only Pipelines

• Research Use Only (RUO) Assays

Software

• Requisition System
• ETL/Dashi (200824-1630)
• Dimsum
• Djerba
• MISO (1.14+)
• Modulator (0.1)
• Pinery (2.13.0+)
• Provenance Client (2.5.17+)
• Provenance records
• Requisition system
• Run Scanner (1.12.0+)
• Shesmu (1.4.2+)
• Vidarr (2.0.3)
• Whizbam
• Other Software

Change Log

Github commit log