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Eligible Datatypes and Workflows

Datatypes eligible for processing

Whole Exome Sequencing

A technique that focuses on sequencing only the exons, which are the coding regions of the genome, of an individual's DNA. WES is used to identify genetic variations in these regions that may be associated with certain diseases or traits.

Whole Genome Sequencing

A technique that involves sequencing the entire genome of an individual. This includes both the coding regions and the non-coding regions of DNA. WGS is used to identify genetic variations throughout the entire genome that may be associated with certain diseases or traits.

Bulk RNA Sequencing

A technique that involves sequencing the transcriptome of a bulk population of cells. This technique provides information on the gene expression levels of all genes in the sample and is commonly used to compare gene expression profiles between different samples or conditions.

Single cell RNA sequencing

A technique that involves sequencing the transcriptome of individual cells. This technique provides information on the gene expression levels of each cell and is commonly used to study cell heterogeneity and identify rare cell populations.

Assay-specific workflow availability

The table below shows the availability of processing workflows for different data files generated through various ‘omics assays. 

Assay
Germline SNV
Somatic SNV
Copy Number Variation (CNV)
Structural variants (SV)
Microsatellite Instability (MSI)
Raw counts
WES
✖️
✖️
:Not_applicable:
WGS
:Not_applicable:
Bulk RNAseq
:Not_applicable:
:Not_applicable:
:Not_applicable:
:Not_applicable:
:Not_applicable:
Single Cell RNAseq
:Not_applicable:
:Not_applicable:
:Not_applicable:
:Not_applicable:
:Not_applicable:
✅ The workflow is available for this datatype
✖️ The workflow is available for this data type, but the NF-OSI will not provide this processing. This decision follows from the recommendation of scientists and engineers at Sage who have worked with these data modalities and have noted various problems in interpretation of processed data from these workflows during downstream analysis. 
:Not_applicable: The workflow is not applicable for this data type.
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