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Software Development

The CCM has Bioinformatics Software Development expertise to help support life sciences projects. We have staff with expertise in computational methods such as Machine Learning and with extensive knowledge of most popular programming languages. Our fees are typically per-project, and depend on its complexity and scope. If your project falls within the overall research aims of one of our affiliate groups we can help enable collaboration by providing software development resources. Please contact us at ccm.contact@sickkids.ca to discuss any potential projects and pricing.

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High Throughput Sequencing Data Analysis

The CCM has extensive expertise in analysis of High-Throughput (a.k.a. NGS) Sequencing data, including both 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, and peak detection and transcription factor binding site analysis for CHIP-Seq.

The CCM team has developed many software packages for many of these problems, and also has extensive expertise in other aspects of HTS data analysis. We can also design custom pipelines for non-model organisms. As developers of state-of-the-art HTS visualization tools such as Savant, we try to make it easy for our users to view the results of our analyses and learn to analyze datasets on their own.

The CCM is playing an active role in developing the first generation of informatics tools to enable the use of whole-genome sequencing in the clinic, as well as providing informatics and data repository support for major sequencing initiatives such as the Finding of Rare Disease Genes (FORGE) Canada project. We have expertise in developing tools for patient phenotyping and custom databases of genomic variants. Please contact us at ccm.contact@sickkids.ca to discuss any potential projects and pricing.