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Bioinformatics Services

CCM Collaborations

The CCM is a full-service bioinformatics lab that offers its expertise in biomedical data analysis to collaborators at SickKids and beyond. We work together with our clients to prepare their datasets for analysis, extract novel insights using a range of statistical and software tools, prepare these results for journal publications and create novel web portals or analysis pipelines for the benefit of the biomedical community. Some of our collaborations are short fee-for-service projects lasting only several days or weeks, while other collaborations span several years and result in multiple joint publications, novel methodologies and new software tools or web resources.

Data Analysis

The CCM has extensive expertise in the analysis of biomedical data: from high-throughput sequencing, to integrated multi-omics analysis, to MRI imaging data, to predictive modelling and machine learning (ML) applications. The CCM plays an active role in developing the first generation of informatics tools to enable the use of whole-genome sequencing in the clinic, and provides informatics and data repository support for major sequencing initiatives such as the Care4Rare project. For ‘omics projects, we perform both the primary data analysis (read mapping and genome assembly) as well as secondary analysis such as variant detection and mutation prioritization for DNA-seq, transcript abundance estimation and identification of alternative/aberrant splicing for RNA-Seq. We also develop custom databases of genomic variants.

Web Portals and Software Tools

The CCM has bioinformatics software development expertise to help support life sciences projects. We have staff with expertise in computational methods and with extensive knowledge of most popular programming languages including Python, R and JavaScript, among others. If your project falls within the overall research aims of the CCM, we can provide software development resources, create new web portals to visualize your datasets, or develop new software pipelines and methodologies that help with the knowledge dissemination for your projects. We try to make it easy for our users to view the results of our analyses and learn to analyze datasets on their own.

Grant Writing and Computational Support

The CCM team can help you in your grant writing in a number of ways. We can provide the computational expertise, an extensive suite of data analysis software and a state-of-the-art high-performance computing infrastructure to support your project. We can make sure that the computational needs of your grant application are well covered, by either serving as co-applicants or by providing a letter of support for your application while also contributing to the grant writing as needed.

High-performance computing

Our high-performance computing team (RIT-HPC) provides services to all labs in SickKids who are interested in using our state-of-the-art facility for data analysis and storage. The CCM team members are experts in using the HPC infrastructure and can offer guidance to other researchers regarding its optimal usage for their needs.   

Bioinformatics Training

Do you want to learn some bioinformatics tools and tricks? Visit the Bioinformatics Training page to learn about our hands-on tutorials.

Service Cost

Please contact us at to discuss any potential projects and pricing. For the bioinformatics analysis priced per sample, there is a $1000 minimum total fee for service if the dataset has only a few samples.

Bioinformatics service Sub-analysis Per sample 
WES data analysisAlignment 
SNV/indel calling and annotation
Report generation 
WGS data analysisAlignment
SNV/indel calling and annotation
SV calling and annotation
STR calling and annotation
Report generation 
Rare variant interpretation  SNVs/indels $130 
Bulk RNAseq data analysisAlignment
Expression and junction quantitation
Differential gene expression
Pathway enrichment analysis 
Other services and consultingBioinformatics and ML data analysis$85/hour (minimum 10 hours)
On-demand trainingCustomized training tutorials$85/hour (minimum 3 hours)