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Bioinformatics : Data Release

Data Release Data release includes transfer of the raw sequence data (fastq format) as it becomes available once sequencing has completed, and the release of analysis files that will vary depending on the services that had been selected. We generally transfer data through a variety of routes: for investigators at OICR or who have access […]

Bioinformatics : Analysis Procedures

In addition to our automated analysis pipelines, the GSI analysis team can also process data through a variety of well-defined analysis procedures. This generally involves an analysis working directly with the project owner to collect the necessary information, then running the tools directly on our high-performance cluster to generate the analysis deliverables. Differential Expression Our […]

BioInformatics : Analysis Pipelines

Analysis Pipeline Details Illumina fastq generation Generation of fastq files from Illumina run folders. This is run on all samples from illumina run folders generated through the Translational Genomics Laboratory, and data return is included as part of the sequencing costs. Analysis : Basecalling and Demultiplexing using Illumina bcl2fastq software. Workflows : bcl2fastq Deliverables : […]

Analysis packages

Analysis Packages Bioinformatics services for research use only (RUO) are offered in three levels of data analysis and return, with increasing costs. We also have accredited assays for clinical trials. Types of RUO analysis: Most of our analysis packages are built as automated pipelines that can be configured to execute as our data comes off […]

Validated pipelines for accredited assays

Whole Genome and Transcriptome Clinical Case Package Our validated tumor-normal whole genome and transcriptome (WGTS) clinical case package includes 80X tumor, 30X normal whole genome and 100M paired end whole transcriptome in one integrated report. A lower coverage version of this package is also available when high tumor purity input is provided (40X tumor, 30X […]

Genome Sequence Informatics

Our system is comprised of a variety of standard analysis workflows, each running a set of tools to accomplish a specific analysis task.  These are organized into standard analysis pipelines, or packages, each composed of one or more consecutive workflows, for both accredited applications as well as research projects. Validated pipelines for accredited assays Our […]