Informatics on High Throughput Sequencing
Date: July 29-30, 2010
Location: Downtown Toronto, ON
Lead Faculty (2010): Asim Siddiqui, Michael Stromberg & Francis Ouellette
Registration Fee for Applications received before June 28, 2010: $500 + GST
Registration Fee for Applications received after June 28, 2010: $700 + GST
Apply now!
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
