Bioinformatics and HPC Core

Bionformatics 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

2017

290

Sequencing runs

2018

265

Sequencing runs

2019

327

Sequencing runs

Services

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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
  • Literature searches
  • Sequence and SNP analysis from raw chromatograms
  • BLAST searches
  • Multiple alignments and trees
  • Primer design
  • Antibody epitope prediction
  • Single cell full data analysis
  • Computer programming
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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 hpc_support@uhnresearch.ca. Please note, the HPC service is for UHN researchers only.

FAQ

Data

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.

Staff

Carl Virtanen

Bioinformatics Core Facility Director
Associate Director, HPC4Health
carl.virtanen@uhnresearch.ca

Natalie Stickle

Core Facility Manager
natalie.stickle@uhn.ca

Zhibin Lu

Bioinformatics & HPC Systems
Administration Manager
zhibin.lu@uhnresearch.ca

Abdellatif Daghrach

Bioinformatician
adaghrach@uhnresearch.ca

Neke Ibeh

Bioinformatician
neke.ibeh@uhnresearch.ca

Qun Jin

Systems Administration/Analyst
qun.jin@uhnresearch.ca

Hyeeun Mok

Technical Analyst
- Web Development
hyeeun.mok@uhnresearch.ca

Gregory Downs

Clinical Team Bioinformatician
gregory.downs@uhnresearch.ca

Roozbeh Dolatshahi

Clinical Team Bioinformatician
roozbeh.dolatashi@uhnresearch.ca

Irene Chae

Clinical Team Bioinformatician
irene.chae@uhnresearch.ca

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
Canada

Phone: (416) 581-7435 or
             (416) 581-7430
Email: hpc_support@uhnresearch.ca

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