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Introduction to Next Generation Sequencing Analysis Part I: Short-read Mapping and Visualization

Date:

Speaker Info:

Phillip Richmond
PhD Student, Wasserman Lab, Centre for Molecular Medicine and Therapeutics
BC Children's Hospital, University of British Columbia

Description

Next generation DNA sequencing has emerged in the past 10 years as an invaluable tool for researchers in the biological sciences. Despite its usefulness, the high-throughput and data intensive nature of this technology has created a roadblock for many biologists who lack formal training in computer science and data analysis.

Luckily for researchers across Canada, UBC’s Advanced Research Computing (ARC) and WestGrid have teamed up to provide hands-on basic analysis workshops that lay the foundation of DNA sequencing analysis. Hosted on the Compute Canada national compute platform—freely available to academic researchers across Canada—the workshop series will lay the foundation for future data analysis projects. Workshops will be hosted in a virtual classroom format, making the content available to researchers across the country.

In the first part of this workshop series, we will be taking a short-read DNA sequencing dataset through genomic alignment and subsequent visualization, both critical steps in the majority of DNA sequencing projects. This workshop places an emphasis on data formats, interacting with the compute server, and using the popular open source bioinformatics tools: BWA, Samtools, and IGV.

Prerequisite Knowledge and Requirements:

  • The primary prerequisite for the course is some past exposure to working in a Linux environment*. For example, during the workshop you will use an SSH terminal client to connect to a remote Linux server, type commands at the Linux shell prompt and will need to be able to view and edit files.
    • * Note: For those interested in the class without Linux experience, a quick primer will be sent out to registered participants. While we encourage participation, the course can also be followed along without executing commands.
  • You need a WestGrid account to participate in this session, however if you do not currently have one, a guest account can be created for you. When you register for the session, please indicate if you require a guest account.

Who Should Attend:

  • Any research faculty, grad students, or university staff interested in learning the basic steps of DNA sequencing analysis and using popular open source bioinformatics tools such as BWA, Samtools, and IGV.