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Bioinformatics and HPC Core

Bioinformatics and High Performance Computing Services

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Welcome to the Bioinformatics and HPC Core

We are a full-service Bioinformatics provider, with services available for analysis of all kinds of high-throughput data, whether generated in house (at one of the UHN Genomics facilities) or externally. A basic data analysis package is available for on a per project basis. Discussion regarding the analysis of your genomics project and experimental design assessments are complimentary.

Sequencing runs we processed



Sequencing runs



Sequencing runs



Sequencing runs


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Basic High-Throughput Sequencing Analysis

Pipelines for analysis should be specifically defined to meet the particular needs of your project but in general it can include:

  • QC analysis of fastq files
  • Alignment to genome
  • QC analysis of aligned reads
  • Standard data processing pipelines (eg. GATK)
  • Variant Calling, for exome or targetted panels
  • Differential gene expression analysis, for RNA-Seq
  • Identification of novel splice variants, for RNA-Seq
  • 10x single cell cellranger pipeline (gene expression, immune profiling, ATAC, …)
  • Methyl-seq pipeline
  • ATAC-seq pipeline
  • HiC-Pro pipeline
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Advanced Data Analysis

Advanced high-throughput sequencing data analysis is also quoted on a per project basis. Advanced data analysis can include:

  • Gene ontology
  • Pathway analysis
  • Single cell data analysis (single cell gene expression, Immune profiling, multiome ATAC + gene expression, CITE-seq, etc)
  • Methyl-seq data analysis
  • Spatial transcriptomics
  • Consistently expanding our workflows to offer a diverse range of data analysis services while incorporating customer feedback.
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High Performance Computing (ONLY available for UHN researchers)

Our group manage UHN HPC clusters. Our clusters contain thousands of cores and several PB storage. Researchers are processing data and performing complex calculations every day on the clusters such as NGS data analysis and machine learning. We also manage software stacks and data sets on the clusters. If you want to use HPC services or have issues on the cluster, please contact Please note, the HPC service is for UHN researchers only.



Please use an FTP client that supports SFTP connections (e.g. FileZilla, sftp or lftp). Enter the Host ip address, port number, username and password provided to you via email. The account is usually valid for 14 days. Please download your data at your earliest convenience and let us know if you have problems downloading the data.


Carl Virtanen

Bioinformatics Core Facility Director
Associate Director, HPC4Health

Natalie Stickle

Core Facility Manager

Zhibin Lu

Bioinformatics & HPC Systems
Administration Manager

Abdellatif Daghrach


Teodora Tockovska


Qun Jin

Systems Administration/Analyst

Hyeeun Mok

Web Developer

Gregory Downs

Clinical Team Bioinformatician

Roozbeh Dolatshahi

Clinical Team Bioinformatician

Irene Chae

Clinical Team Bioinformatician

Matthew Stoodley

Clinical Team Bioinformatician

Contact Us

Bioinformatics and HPC Core

The Bioinformatics and HPC Core is located at:

Princess Margaret Cancer Research Tower
101 College Street, Rm 11-707
Toronto, Ontario, M5G 1L7

Phone: (416) 581-7435 or
             (416) 581-7430

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