Bioinformatician - The Centre for Applied Genomics

The Hospital for Sick Children
Toronto, ON, Canada
Job Type:
  • Staff (Temporary contract of one year, with possibility of renewal/transition to permanent)
Degree Level Required:
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Bioinformatician - The Centre for Applied Genomics

The Centre for Applied Genomics (TCAG; is seeking bioinformaticians to implement large-scale analyses of high-throughput sequencing data, for a variety of research projects led by investigators at The Hospital for Sick Children and around the world.

JOB DESCRIPTION TCAG is a world-leading genomics facility located in the Research Institute of The Hospital for Sick Children in Toronto. It is also a part of CGEn, Canada’s national facility for genome sequencing and analysis. Our Sequencing Facility provides DNA sequencing services to a wide variety of public and private research institutions, using the latest sequencing platforms and technologies from Illumina, PacBio, and other vendors. We seek qualified bioinformaticians to work with our Informatics and Biostatistics group to implement best-practices analysis, quality control, and data management pipelines, for the high volume of projects and samples sequenced on these platforms. This essential role is at the interface of laboratory and high performance computing, shepherding clients’ data from the instruments through complex, multi-stage analyses on our local HPC cluster, and preparing final reports and data packages for delivery to each client.

ABOUT SICKKIDS Dedicated exclusively to children and their families, The Hospital for Sick Children (SickKids) is one of the largest and most respected paediatric healthcare centres in the world. As innovators in child health, we lead and partner to improve the health of children through the integration of healthcare, leading-edge research and education. Our reputation would not have been built – nor could it be maintained – without the skills, knowledge and experience of the extraordinary people who come to work here every day. SickKids is committed to ongoing learning and development, and features a caring and supportive work environment that combines exceptionally high standards of practice.

When you join SickKids, you become part of our community. We share a commitment and determination to fulfill our vision of Healthier Children. A Better World.

Don’t miss out on the opportunity to work alongside the world’s best in paediatric healthcare.

OUR COMMITMENT TO DIVERSITY The children and families we care for are diverse, and so are our employees. All are welcome to join our unique organizational culture and be part of our inclusive team.

If requested, SickKids is proud to make available accommodations to support applicants with disabilities during the interview and assessment process. Information received relating to accommodation will be addressed confidentially. SickKids is also committed to providing services in both official languages and our preference is to hire employees who are fluent in both English and French whenever possible.

Thank you for your interest in joining SickKids. Only those applicants selected for an interview will be contacted. In accordance with our Hospital policy, employment at SickKids is conditional upon the Hospital’s receipt of all necessary documentation.


  • Develop and execute software pipelines to take raw intensity output from high-throughput DNA sequencers through base-calling, genome alignment, variant calling, and annotation stages;
  • Prepare reports for customers and collaborators;
  • Track and manage data and analyses for many hundreds of samples and multiple projects at any one time;
  • Work with sequencing experts from multiple hospital facilities and affiliated institutions to improve and standardize analysis pipelines used for both basic and applied research projects; and
  • Work with both the sequencing facility and the informatics group to streamline processing and quality assurance as we scale up to many thousands of genomes per year.


Required skills include the development and maintenance of Python/Perl HPC pipelines for analyses, monitoring and troubleshooting the operation of processes in a large Unix HPC cluster environment, data management, and technical writing.

  • BSc or higher degree in bioinformatics, computer science, or a related discipline
  • Familiarity with current best practices and software tools for analyzing high-throughput sequence data (e.g. GATK, Picard, BWA, Annovar, IGV)
  • Ability to work with and interpret raw sequence reads, alignments, features, variant calls, and assemblies, in commonly used data formats (fasta/fastq, sam/bam, bed, vcf)
  • Solid and demonstrated programming skills, particularly in Python, Perl and bash shell
  • Strong organizational skills; this position requires tracking and managing many large and small projects for collaborators and internal researchers
  • Strong oral, written, and interpersonal communication skills
  • A true team approach and collegial attitude.

Additional Information


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