Explore

Genome Assembly Programming Challenge

Approx. 18 hours to complete

Save Course

Go to Course

Course Summary

This course teaches how to assemble genomes from short DNA sequences. Students will learn the algorithms and software used to assemble genomes, as well as the challenges and limitations of the process.

Key Learning Points

Learn about the algorithms and software used to assemble genomes
Understand the challenges and limitations of genome assembly
Gain hands-on experience with genome assembly software

Learning Outcomes

Understand the principles of genome assembly
Learn to use genome assembly software and interpret the results
Gain the skills to independently assemble a genome

Prerequisites or good to have knowledge before taking this course

Basic knowledge of molecular biology and genetics
Familiarity with programming in Python

Course Difficulty Level

Intermediate

Course Format

Online
Self-paced

Similar Courses

Structural Bioinformatics
Genomic Data Science
Bioinformatics

Related Education Paths

Notable People in This Field

Director of EMBL-EBI and Deputy Director-General of EMBL
President & Founding Director, Broad Institute of MIT and Harvard

Related Books

Description

In Spring 2011, thousands of people in Germany were hospitalized with a deadly disease that started as food poisoning with bloody diarrhea and often led to kidney failure. It was the beginning of the deadliest outbreak in recent history, caused by a mysterious bacterial strain that we will refer to as E. coli X. Soon, German officials linked the outbreak to a restaurant in Lübeck, where nearly 20% of the patrons had developed bloody diarrhea in a single week. At this point, biologists knew that they were facing a previously unknown pathogen and that traditional methods would not suffice – computational biologists would be needed to assemble and analyze the genome of the newly emerged pathogen.

To investigate the evolutionary origin and pathogenic potential of the outbreak strain, researchers started a crowdsourced research program. They released bacterial DNA sequencing data from one of a patient, which elicited a burst of analyses carried out by computational biologists on four continents. They even used GitHub for the project: https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/wiki The 2011 German outbreak represented an early example of epidemiologists collaborating with computational biologists to stop an outbreak. In this Genome Assembly Programming Challenge, you will follow in the footsteps of the bioinformaticians investigating the outbreak by developing a program to assemble the genome of the E. coli X from millions of overlapping substrings of the E.coli X genome.

Outline

The 2011 European E. coli Outbreak
2011 European E. coli outbreak
Assembling phage genome
About University
What does it mean to assemble a genome?
Project Description
Rules on the academic integrity in the course

Assembling Genomes Using de Bruijn Graphs
DNA arrays
Assembling genomes from k-mers
De Bruijn graphs
Bridges of Königsberg and universal strings
Euler theorem

Genome Assembly Faces Real Sequencing Data
Splitting the genome into contigs
From reads to read-pairs
Genome assembly faces real sequencing data

Summary of User Reviews

Pros from User Reviews

Hands-on experience provided
Practical approach to understanding genome assembly
Clear and concise lectures
Good pace of the course
Helpful course material

Cons from User Reviews

Some users found the course too basic
Not suitable for advanced learners
Limited discussion on recent advances in genome assembly
Some technical issues with the platform
Course could be more interactive

Recommended for you

Algorithms for DNA Sequencing

We will learn computational methods -- algorithms and data structures -- for analyzing DNA sequencing data. We will learn a little about DNA, genomics, and how DNA sequencing is used....

Save Course