Genome Assembly Programming Challenge

Go to Course: https://www.coursera.org/learn/assembling-genomes

Introduction

### Course Review and Recommendation: Genome Assembly Programming Challenge **Overview** The "Genome Assembly Programming Challenge" course on Coursera offers a unique and timely exploration into the world of bioinformatics through the lens of a real-world medical crisis: the 2011 European E. coli outbreak. This course immerses students in the urgent need for genomic sequencing in epidemiology, showcasing how computational biology can be pivotal in solving critical health challenges. It skillfully interweaves opportunities for practical learning with substantive scientific knowledge to empower learners in the field of genome assembly. **Course Content and Structure** The course is structured into three substantive modules, each building on concepts from the previous one, ensuring a cohesive learning experience: 1. **The 2011 European E. coli Outbreak**: This foundational module sets the stage for understanding the outbreak and emphasizing the essential question: “What is the genome sequence of E. coli X?” Here, learners are introduced to the importance of rapid genomic sequencing in outbreak management and treatment development. 2. **Assembling Genomes Using de Bruijn Graphs**: This module dives deeper into the methodologies used in DNA sequencing, specifically focusing on de Bruijn graphs. It discusses the evolution of genome sequencing practices and introduces students to k-mer analysis, an essential concept for genomic assembly. To add an enriching perspective, learners are also prompted to solve a jigsaw puzzle-like problem, connecting historical mathematics with modern computational biology. 3. **Genome Assembly Faces Real Sequencing Data**: The final module tackles the practical challenges of genomic assembly that arise from modern sequencing technologies. Students will get their hands dirty by assembling the smallest bacterial genome, providing invaluable experience before tackling the assembly of the E. coli X genome. This practical aspect reinforces theoretical knowledge, grounding concepts in real-world applications. **Learning Outcomes** Upon completing this course, students will have gained: - A solid understanding of genomic sequencing and assembly techniques. - Practical experience in developing algorithms for genome assembly. - Insight into the collaborative roles of bioinformaticians and epidemiologists in tackling public health crises. - Hands-on exposure to real sequencing data and the associated challenges in modern computational biology. **Recommendation** I wholeheartedly recommend the "Genome Assembly Programming Challenge" for anyone interested in bioinformatics, genomics, or public health. This course does not merely regurgitate information; it offers an interactive and engaging way to understand complex biological concepts through practical programming challenges. Whether you are a student aspiring to enter the field, a bioinformatics professional seeking to refresh your knowledge, or simply a curious mind interested in how technology and biology converge in crisis management, this course will equip you with both theoretical insights and practical skills. The blend of historical context, algorithmic challenges, and real-world application creates a robust educational experience that is relevant and often critical in today’s scientific landscape. Enroll today, and start assembling not just genomes, but also a deeper understanding of one of biology's most exciting frontiers!

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.

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!

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!