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Genome Assembly Programming Challenge, University of California San Diego

87 ratings
25 reviews

About this Course

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: 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....

Top reviews


Aug 05, 2018

I would like to say thank you to all who have created this course and specialization! Good material, excellent lecturers!


Aug 04, 2017

Good course and final capstone project. Would recommend anyone from beginner to professional.

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25 Reviews

By Zac Bolton

Oct 04, 2018

Most challenging course I've taken on Coursera so far, so be prepared. However, I'm definitely a far better programmer due to it! <3 Thanks to the instructors for great material and well designed challenges.

By Joseph Gonzalez Nowak

Sep 19, 2018

Nice exercises were difficult and interesting. You can learn a lot of in this course not only to solve bioinformatic problems

By Alexandr Semuka

Aug 05, 2018

I would like to say thank you to all who have created this course and specialization! Good material, excellent lecturers!

By Henry Read

Jul 28, 2018

Not bad, but you had better attend Bioinformatics Specialization so you could understand what tutors lecture.

By John Berkowitz

Jun 15, 2018

There were countless errors in the descriptions of the programming problems, not just "ambiguities" or "open ended problem definitions" but quantitatively incorrect specific statements (length of inputs, structure of inputs, etc). Many of these issues have been pointed out in the forums, but remain uncorrected as of June 2018.

By Alexander Chertov

Jun 08, 2018

I did not enjoy this course. I did not like the following things:1) It was advertizing a different course (Bioinformatics or something like that) too hard for my taste.2) The problem statements were often incorrect. In particular what is related to the size of inputs. I have wasted too much time because of these issues. For example, the problem statement says that there will be 400 lines of input. After wasting an hour and a half trying to find a cause of a segmentation error I am reading on the forum a message THAT IS ONE YEAR OLD saying that there are in fact 1618 lines of input.3) The final problem (genome assembler) has a very tight memory limit if you consider the size of the input. Solving it within the memory limit would require special skills that are not covered by the material in this course. Or maybe I (and other people on the forum) are just not smart enough.4) There are almost no lectures. All you have to work with seems to be a 60-page extract from a book.

By Pablo Esau Mejia Medina

Jun 03, 2018

Greate course

By Fabrice Lacout

Apr 28, 2018

A bit too challenging. A this point after 5 courses you just want to have a cool capstone and receive your certificate.

By Tamilarasu S

Apr 25, 2018

Very good collection of problems for a finale.

Though you would not be assembling human genome, you will be exposed to the challenges faced during a real genome assembly of a bacterial genome.

A very theoretical specialization ending with practical problems.

By Suresh Balasubramanian

Apr 01, 2018

Excellent assignments - a great capstone course to complete the data structures and algorithms specialization. The assignments make sure that you go back and revise the concepts you learnt early in the specialization as they need an in-depth understanding of the concepts taught earlier. But be prepared to take some hardship, spend that extra effort and break your brain in fine-tuning your solutions. Highly recommended...