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Building a fully-fledged algorithm to assemble genomes from DNA fragments on a real dataset is an enormous challenge with major demand in the multi-billion dollar biotech industry.
In this capstone project, we will take the training wheels off and let you design your own optimized software program for genome sequencing.
This big data challenge will cover the entire MicroMasters program. After a brief introduction to the steps required to build a genome assembler, we will let you take steps on your own to start working with real data taken from a sequencing machine and see if you can design genome assembly software that can compete with popular software used in hundreds of sequencing labs around the world every day.
- Graph algorithms
- Algorithms for genome assembly
- Algorithm optimization
Prerequisite
Basic knowledge of:
- at least one programming language: loops, arrays, stacks, recursion.
- mathematics: proof by induction, proof by contradiction.
Syllabus
This big data challenge will cover the entire program. After a brief introduction to the steps required to build a genome assembler, we will let you take steps on your own to start working with real data taken from a sequencing machine and see if you can design genome assembly software that can compete with popular software used in hundreds of sequencing labs around the world every day.
Instructors
Pavel Pevzner
Ronald R. Taylor Professor of Computer Science
The University of California, San Diego
Phillip Compeau
Assistant Teaching Professor
Carnegie Mellon University
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