Course Description

Next generation DNA sequencing technology has revolutionized our ability to ask almost any question of our genome, epigenome or transcriptome. In Part I of this Module, we focus on the principles of the dominant technology: the Illumina short read sequencing by synthesis platform. The complete analysis pipeline is examined in detail, from the generation of raw reads, through alignment to the genome (Part II), and up to gene-centric analyses in Part III. At each step, there will be a strong emphasis on quality control, highlighting limitations and common pitfalls of the most commonly used tools, as well as ways to deal with them. In Part IV, alternate DNA sequencing technologies are surveyed, showcasing their applications.

Students will use the knowledge gained throughout this Module to apply to a practical project which will focus on the integration of multiple NGS data types to address a biomedically relevant question.

Course Objectives

After completing this Module, students will be able to:

Have a deep appreciation of current DNA sequencing technologies, and an awareness of pitfalls, caveats, and confounding factors;
Understand which technologies are appropriate for which use cases;
Be aware of the details in deriving insights from raw data;
Be able to critically assess next generation sequencing data and analyses, and be aware of common biases.

Assignments/Assessment

60% of the grade will be assessed by an individual project, using techniques learned in class to explore a meaningful biological question. The project will be developed throughout the course, with opportunities every week to refine and get feedback. 40% of the grade will be assessed via weekly short programming exercises.

Grading

Students in Master’s programs will receive a letter grade (A-F); students in PhD programs will be graded using the Weill Cornell Graduate School grading system (Honors, High Pass, Low Pass, Fail).

Teaching Assistants

There will be one teaching assistant for this course: Mervin Fansler.