April 27 - May 3, 2015
Application Deadline: March 1, 2015

In collaboration with the Canadian Bioinformatics Workshops and the New York Genome Center

This course will take place in New York City at the main campus of the New York Genome Center (NYGC) - Travel details

Lead Faculty:
Guillaume Bourque, Matei David, Marc Fiume, Francis Ouellette, Jared Simpson, Malachi Griffith, Obi Griffith,
Lincoln Stein, Juri Reimand, Quaid Morris, Irina Kalatskaya, Robin Haw, and Michael Hoffman

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, in collaboration with Cold Spring Harbor Laboratory and the New York Genome Center, 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.

The course combines the material and concepts from three established workshops (see a full outline here):
1.Informatics on High-Throughput Sequencing Data
2.Informatics for RNA-Seq Analysis
3.Pathway & Network Analysis of -omic Data

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. Click here for the full course outline from the Canadian Bioinformatics Workshops.

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; 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.

Application instructions: Follow the link above to apply for this course. One letter of recommendation is required along with a personal statement; a CV is strongly encouraged. In your statement, you should demonstrate a need for the course material by describing both your academic background and the research project which requires the concepts and tools covered in the course. Admission decisions will be returned the week of March 9th.

Tuition: $2,600

The course will run from 8:30 a.m. until 5 p.m. each day. Course fees cover registration and all food except dinners (i.e., continental breakfasts, coffee breaks, lunches, and a reception). Housing and transportation to and from the New York Genome Center are not included. Payment is not required until you have completed the full application process and are accepted into the course. Full payment is due on April 10th. A receipt will be included in each course packet, available upon check-in at the New York Genome Center on April 27th.

Cancellations after April 10th will incur cancellation charges of $150. No-shows are ineligible for any refunds except in extenuating circumstances. If you have difficulties arranging payment, contact the Course Registrar without fail; your place in the course may be at risk if payment is not received on time. If you must cancel or if someone else will take your slot in the course, please notify the Course Registrar.

If you would rather not apply for the course at this time but would like to express interest in applying for a future course, click below. Filling out this form is not binding; it simply confirms your interest in the course, which helps us plan for and anticipate future course needs.