Genome Assembly Programming Challenge from Coursera

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 online course 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.

What's inside

Syllabus

The 2011 European E. coli Outbreak

In April 2011, hundreds of people in Germany were hospitalized with a deadly disease that often started as food poisoning with bloody diarrhea. 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. Within a few months, the outbreak had infected thousands and killed 53 people. To prevent the further spread of the outbreak, computational biologists all over the world had to answer the question “What is the genome sequence of E. coli X?” in order to figure out what new genes it acquired to become pathogenic. 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 deadly E. coli X strain. However, before you embark on building a program for assembling the E. coli X strain, we have to explain some genomic concepts and warm you up by having you solve a simpler problem of assembling a small virus.

Assembling Genomes Using de Bruijn Graphs

DNA sequencing approach that led to assembly of a small virus in 1977 went through a series of transformations that contributed to the emergence of personalized medicine a few years ago. By the late 1980s, biologists were routinely sequencing viral genomes containing hundreds of thousands of nucleotides, but the idea of sequencing a bacterial (let alone the human) genome containing millions (or even billions) of nucleotides remained preposterous and would cost billions of dollars. In 1988, three biologists (independently and simultaneously!) came up with an idea to reduce sequencing cost and proposed the futuristic and at the time completely implausible method of DNA arrays. None of these three biologists could have possibly imagined that the implications of his own experimental research would eventually bring him face-to-face with challenging algorithmic problems. In this module you will learn about the algorithmic challenge of DNA sequencing using information about short k-mers provided by DNA arrays. You will also travel to the 18the century to learn about the Bridges of Konigsberg and solve a related problem of assembling a jigsaw puzzle!

Genome Assembly Faces Real Sequencing Data

Our discussion of genome assembly has thus far relied upon various assumptions. In this module, we will face practical challenges introduced by quirks in modern sequencing technologies and discuss some algorithmic techniques that have been devised to address these challenges. Afterwards, you will assemble the smallest bacterial genome that lives symbiotically inside leafhoppers. Its sheltered life has allowed it to reduce its genome to only about 112,091 nucleotides and 137 genes. And afterwards, you will be ready to assemble the E. coli X genome!

Good to know

Know what's good

, what to watch for

, and possible dealbreakers

Features a hands-on assembly programming challenge to assemble the genome of E. coli X, providing learners with practical experience in genome assembly

Taught by highly accomplished instructors Pavel Pevzner, Alexander S. Kulikov, Neil Rhodes, and Michael Levin, who are recognized for their work in the field of bioinformatics

Explores the 2011 European E. coli Outbreak, a real-world example of how epidemiologists and computational biologists collaborated to stop an outbreak

Develops core skills in genome assembly and computational biology, which are in high demand in the fields of bioinformatics, medicine, and research

Suitable for learners with a background in biology, computer science, or a related field

Requires learners to have some familiarity with bioinformatics concepts and tools, but provides resources for those who need a refresher

Reviews summary

Engaging capstone in bioinformatics

Learners say this challenging capstone is great and very rewarding. The course pulls together everything learned in bioinformatics and makes it come together. Learners note that the assignments are difficult but feel that it is worth the effort. Some learners also wish there was more information available for the assignment.

Learners find the capstone very rewarding.

"Excellent."

"Great course, hard but it is worth."

"It was great! Really tough, but rewarding."

Learners wish there was more information available for the assignments.

"The last assignment was extremely frustrating."

"hi, this is a hard course and the videos are not sufficient."

"You're on your own here about how you approach the problems, although there is some nice supplemental material available in the form of introductory videos and a booklet walking you through the project."

Learners say this course is very challenging.

"Too hard."

"Why we are learn this is biology part"

"It is a challenging course, which makes it great."

Activities

Be better prepared before your course. Deepen your understanding during and after it. Supplement your coursework and achieve mastery of the topics covered in Genome Assembly Programming Challenge with these activities:

Review Sequencing Technology Concepts

Show steps

Refresh your memory on the core concepts of DNA sequencing. This will make learning about genome assembly in this course easier.

Browse courses on DNA Sequencing

Show steps

Read a short summary of the Sanger sequencing method
Watch a video on next-generation sequencing methods
Review your notes or textbook on sequencing technologies

Learn about de Bruijn graphs

Show steps

A de Bruijn graph is a data structure that is central to genome assembly. Working through a tutorial on it will strengthen your understanding of this concept.

Show steps

Find a tutorial on de Bruijn graphs
Work through the tutorial, taking notes
Try to apply the concepts you learned to a simple example

Participate in the course discussion forums

Show steps

Helping others understand genome assembly will reinforce your own learning and identify areas you need to improve.

Show steps

Visit the course discussion forums
Answer questions asked by other students
Ask for help if you have questions
Provide feedback on other students' responses

Four other activities

Expand to see all activities and additional details

Show all seven activities

Practice assembling small sequences using de Bruijn graphs

Show steps

Getting hands-on experience with assembling small sequences will prepare you for developing your own assembler for E. coli X.

Show steps

Find a practice problem or dataset with small sequences
Assemble the sequences using a de Bruijn graph
Check your results

Attend a workshop on genome assembly

Show steps

Attending a workshop will provide you with insights from experts in the field and allow you to network with other professionals.

Show steps

Find a workshop on genome assembly that fits your schedule and interests
Register for the workshop
Attend the workshop and participate actively
Follow up with any contacts you make at the workshop

Build a genome assembler in your favorite programming language

Show steps

Applying your knowledge to build something concrete will help you deeply understand genome assembly. You'll also develop valuable coding skills.

Show steps

Choose a programming language
Design the architecture of your assembler
Implement the assembler
Test your assembler on small sequences
Optimize your assembler for performance

Volunteer at a local biotech lab

Show steps

Working in a lab will provide hands-on experience in the techniques and technologies used in genome assembly.

Show steps

Find a local biotech lab that is willing to take volunteers
Contact the lab and ask about volunteer opportunities
Complete any required training or orientation
Perform tasks assigned by the lab staff

Career center

Learners who complete Genome Assembly Programming Challenge will develop knowledge and skills that may be useful to these careers:

Genome Assembler

Genome assemblers are responsible for assembling genomes from raw sequencing data. This is a complex and challenging task, as genomes are often large and complex. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Genome Assembly.

See salaries and explore the career path for Genome Assembler

Computational Biologist

Computational Biology is the study of biology using mathematical and computational techniques. It combines computer science, applied mathematics, biology, and software engineering to understand biological systems. The Genome Assembly Programming Challenge is a course designed to teach students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Computational Biology.

See salaries and explore the career path for Computational Biologist

Bioinformatics Scientist

Bioinformatics is the use of computer science and information technology to analyze and interpret biological data. Bioinformatics is used in a variety of fields, including genetics, genomics, and drug discovery. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Bioinformatics.

See salaries and explore the career path for Bioinformatics Scientist

Biomedical Engineer

Biomedical engineers use engineering principles to design and build medical devices and equipment. They also work on developing new treatments and therapies for diseases. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Biomedical Engineering.

See salaries and explore the career path for Biomedical Engineer

Biostatistician

Biostatisticians use statistical methods to analyze biological data. They work on a variety of projects, including drug development, clinical trials, and public health research. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Biostatistics.

See salaries and explore the career path for Biostatistician

Molecular Biologist

Molecular biologists study the structure and function of molecules, such as DNA, RNA, and proteins. They work on a variety of projects, including gene expression, genetic engineering, and drug development. Genome assembly is a central technique in molecular biology and is essential for understanding the genetic makeup of living organisms.

See salaries and explore the career path for Molecular Biologist

Researcher

Researchers conduct scientific research to advance knowledge and understanding. They work on a variety of projects, including basic research, applied research, and development. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Research.

See salaries and explore the career path for Researcher

Data Scientist

Data scientists use data to solve problems. They work on a variety of projects, including fraud detection, customer segmentation, and product development. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Data Science.

See salaries and explore the career path for Data Scientist

Microbiologist

Microbiologists study microorganisms, such as bacteria, viruses, and fungi. They work on a variety of projects, including infectious disease research, drug development, and environmental microbiology. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Microbiology.

See salaries and explore the career path for Microbiologist

Geneticist

Geneticists study genes and heredity. They work on a variety of projects, including genetic testing, gene therapy, and the development of new drugs. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Genetics.

See salaries and explore the career path for Geneticist

Pharmaceutical Scientist

Pharmaceutical scientists develop and test new drugs. They work on a variety of projects, including drug discovery, drug development, and clinical trials. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Pharmaceutical Science.

See salaries and explore the career path for Pharmaceutical Scientist

Physician

Physicians diagnose and treat diseases. They work on a variety of projects, including patient care, research, and teaching. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Medicine.

See salaries and explore the career path for Physician

Medical Physicist

Medical physicists use physics to develop and improve medical treatments. They work on a variety of projects, including cancer treatment, imaging, and radiation therapy. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Medical Physics.

See salaries and explore the career path for Medical Physicist

Software Engineer

Software engineers design, develop, and maintain software applications. They work on a variety of projects, including web development, mobile development, and data science. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Software Engineering.

See salaries and explore the career path for Software Engineer

Epidemiologist

Epidemiologists study the distribution and determinants of health-related states or events (including disease), and the application of this study to the control of diseases and other health problems. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Epidemiology.

See salaries and explore the career path for Epidemiologist