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
• Change Log

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
• Change Log
• 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

• June CR-119 update (#14) by Morgan Taschuk at 2026-07-21 19:22:33

  * Remove references to mini-Djerba * Improve changelogs by pulling in the actual changes for each page with sphinx-git

• Update tar assay to 4.0; move shallow whole genome to RUO pipelines s… (#4) by Morgan Taschuk at 2025-10-23 20:04:08

  …ection

• Update tar assay to 4.0; move shallow whole genome to RUO pipelines section by Morgan Taschuk at 2025-10-16 18:59:56

• Add changelogs to every page; add a note about identical amended reports for CAPA-221 by Morgan Taschuk at 2025-09-15 20:10:46

• Reorganized so each SOP has its own section by Morgan Taschuk at 2025-08-18 19:08:34

• Reduce the depth of the toctree on this page by Morgan Taschuk at 2025-08-18 15:59:02

• First draft of migrating Data Review and Reporting Procedure to the site by Morgan Taschuk at 2025-08-18 15:55:39

• Fix errors by Morgan Taschuk at 2025-08-13 14:02:41

• start work on data review and reporting by Morgan Taschuk at 2025-08-12 19:32:09

• consolidating informatics pieplines into one document by Morgan Taschuk at 2025-08-12 15:08:23

• First draft of informatics pipelines by Morgan Taschuk at 2025-06-26 02:07:03

• Converted to Sphinx and readthedocs by Morgan Taschuk at 2025-06-23 15:30:35

• View detailed change log