With the introduction of next-generation sequencing platforms, it is now feasible to use high-throughput sequencing approaches to address many research questions. Now more than ever, it is crucial to know what bioinformatic tools and resources are available, and it is necessary to develop informatic skills to analyze high-throughput data using those tools. The Canadian Bioinformatics Workshops (CBW), in collaboration with Cold Spring Harbor Laboratory, has developed a comprehensive seven-day course covering key bioinformatics concepts and tools required to analyze DNA- and RNA-sequence reads using a reference genome. This course combines the material and concepts from three established CBW workshops; see a full outline here.
The course will begin with the workflow involved in moving from platform images to sequence generation, after which participants will gain practical skills for evaluating sequence read quality, mapping reads to a reference genome, and analyzing sequence reads for variation and expression level. The course will conclude with pathway and network analysis on the resultant 'gene' list. Participants will gain experience in cloud computing and data visualization tools. All class exercises will be self-contained units that include example data (e.g., Illumina paired-end data) as well as detailed instructions for installing all required bioinformatics tools.
Target Audience: Graduate students, postdoctoral scholars, and principal investigators currently working with data from next-generation sequencing platforms, or about to embark on projects that require analysis of such data. The course will focus mainly on data generated by Illumina machines. A reference genome is required; the course will not cover de novo assembly of sequence reads from organisms that do not already have a reference genome.
Prerequisites: You must have basic familiarity with Linux environments and S, R, or Matlab to participate in this course. Everyone will need to complete and understand the following tutorials before attending the course: 1) Linux Tutorial for Beginners; and, 2) Quick & Dirty Guide to R.
Computer requirements: If selected for the course, you will need to bring your own laptop computer with wireless internet capacity. The minimum specifications are as follows: 1024x768 screen resolution, 1.5GHz CPU, 1GB RAM, and a recent version of the Windows, Mac OS X or Linux operating systems. Most laptops purchased in the past 3-4 years likely meet these requirements. If you do not have access to your own laptop, you may be able to borrow one from CSHL.
Confirmed Speakers and Module Instructors:
Mathieu Bourgey, McGill University
Florence Cavalli, University of Toronto
Malachi Griffith, Washington University School of Medicine
Obi Griffith, Washington University School of Medicine
Robin Haw, Ontario Institute for Cancer Research
Michael Hoffman, Princess Margaret Cancer Center
Quaid Morris, University of Toronto
Juri Reimand, Ontario Institute for Cancer Research
Jared Simpson, Ontario Institute for Cancer Research
Veronique Voisin, University of Toronto
Fouad Yousif, Ontario Institute for Cancer Research
Support & Financial Aid
Major support for this course is generously provided by the Helmsley Charitable Trust
Access to cloud computational resources may be supported by an education grant from Amazon Web Services
Financial aid is available to help offset tuition costs as follows:
1) Interdisciplinary Fellowships (transitioning from outside biology) & Scholarships (transitioning from other biological disciplines) are provided by the Helmsley Charitable Trust
2) Financial aid for international applicants is provided by the Howard Hughes Medical Institute
Please indicate your eligibility for either of these funding sources in a financial aid request submitted as part of your application materials. Financial aid requests do not affect selection decisions made by the instructors.
Cost (including board and lodging): $2,855
The following button links to a short form which confirms your interest in the course, but is not an official application form. To apply to the course, click the Application tab above. No fees are due until you have completed the full application process and are accepted into the course.
Students accepted into the course should plan to arrive in Cold Spring Harbor by the evening of March 19 and depart after lunch on March 26.