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Informatics on High Throughput Sequencing

Workshop Details
Date: July 23-24, 2009
Location: Downtown Toronto, ON
Lead Faculty (2009): Asim Siddiqui, Michael Brudno, Michael Stromberg & Francis Ouellette
Registration Fee: $500 + GST
SOLD OUT for 2009

Target Audience
This workshop is geared to graduate students, post-doctoral fellows, clinical fellows and investigators involved in analyzing data from HT sequencing platforms.

Prerequisite: Your own laptop computer. If you do not access to a laptop, you may loan one from the CBW for a fee. Please contact course_info@bioinformatics.ca for more information.

Course Objectives
With the introduction of high-throughput sequencing platforms from Illumina, Roche and ABI, it is becoming feasible to consider sequencing approaches to address many research projects. However, knowing how to manage and interpret the large volume of sequence data resulting from such technologies is less clear. The CBW has developed a 2-day course covering the bioinformatics tools available for managing and interpreting high-throughput sequencing data.

Beginning with an understanding of the workflow involved to move from platform images to sequence generation, participants will gain practical experience and skills to be able to:

  • Assess sequence quality
  • Map sequence data onto a reference genome
  • Quantify sequence data
  • Integrate biological context with sequence information

Course Outline

Day 1
Module 1: Introduction to next generation sequencing (Faculty: Francis Ouellette)

  • Types of platforms
  • Common applications and issues

Break (30 minutes)

Module 2: Genome assembly (Faculty: Michael Brudno)

  • How do you assemble a genome?
  • What are the issues with short reads?
  • De-novo versus reference-assisted assembly

Lunch

Module 3: Genome variation - SNPs (Faculty: Michael Stromberg)

  • Single Nucleotide Polymorphism (SNP) Sequence Data

Break (30 minutes)

  • Laboratory - Genome Variation

Dinner

  • Open Lab

Day 2
Module 4: Large Scale Genome Variation (Faculty: Michael Brudno)

  • Structural Genome Variations/Chromosome rearrangements
  • Copy Number Variations (CNVs)

Break (30 minutes)

Laboratory Assignment

  • Perform a genome Assembly

Lunch

Module 5: Whole Transcriptome & RNA-Sequencing (Faculty: Asim Siddiqui)

  • How do you analyze data from RNA experiments?
  • How do they compare to other technologies e.g. microarrays, RT-PCT?

Break (30 minutes)

Module 6: Data management (Faculty: Asim Siddiqui)

  • Data centre fundamentals: dealing with data, tips and tricks
  • Data standards

Pre-Readings
http://www.ncbi.nlm.nih.gov/pubmed/18576944
http://www.ncbi.nlm.nih.gov/pubmed/18349386