Whole genome sequencing of bacterial genomes - tools and applications from Coursera

This course will cover the topic of Whole genome sequencing (WGS) of bacterial genomes which is becoming more and more relevant for the medical sector. WGS technology and applications are high on international political agenda, as the classical methods are being replaced by WGS technology and therefore bioinformatic tools are extremely important for allowing the people working in this sector to be able to analyze the data and obtain results that can be interpreted and used for different purposes. The course will give the learners a basis to understand and be acquainted with WGS applications in surveillance of bacteria including species identification, typing and characterization of antimicrobial resistance and virulence traits as well as plasmid characterization. It will also give the opportunity to learners to learn about online tools and what they can be used for through demonstrations on how to use some of these tools and exercises to be solved by learners with use of freely available WGS analysis tools .

By the end of this course you should be able to:

1. Describe the general Principles in typing of Bacteria

2. Give examples of the applications of Whole Genome Sequencing to Surveillance of bacterial pathogens and antimicrobial resistance

3. Apply genomic tools for sub-typing and surveillance

4. Define the concept of Next-Generation Sequencing and describe the sequencing data from NGS

5. Describe how to do de novo assembly from raw reads to contigs

6. Enumerate the methods behind the tools for species identification, MLST typing and resistance gene detection

7. Apply the tools for species identification, MLST typing and resistance gene detection in real cases of other bacterial and pathogen genomes.

8. Describe the methods behind the tools for Salmonella and E.coli typing, plasmid replicon detection and plasmid typing

9. Utilize the tools for Salmonella and E.coli typing, plasmid replicon detection and plasmid typing in real cases of other bacterial and pathogen genomes.

10. Explain the concept and be able to use the integrated bacterial analysis pipeline for batch analysis and typing of genomic data

11. Demonstrate how to construct phylogenetic tree based on SNPs

12. Apply the phylogenetic tool to construct phylogenetic trees and explain the relatedness of bacterial or pathogen strains

13. Describe how to create your own sequence database

14. Utilize the MyDbFinder tool to detect genetic markers of interest from whole genome sequencing

What's inside

Syllabus

Module 1

Welcome and introduction to typing of bacteria and use of Whole genome sequencing applied to surveillance of bacterial pathogens and antimicrobial resistance

Module 2

Introduction to Next Generation sequencing

Module 3

Whole genome sequencing tools- demonstration of analysis tools for species identification, MLST typing and finding resistance genes

Module 4

Whole genome sequencing tools- demonstration of analysis tools for Serotyping of Salmonella and Escherichia coli strains , and finding plasmid replicons

Module 5

Whole genome sequencing tools- demonstration of analysis tools for multiple analyzes, phylogenetic tree building and finding genetic markers from self-made databases and Summative Tutorial exercise

Good to know

Know what's good

, what to watch for

, and possible dealbreakers

Explores Whole genome sequencing technology and its applications, which is highly relevant for the medical sector

Develops skills to analyze genomic data for species identification, MLST typing, and resistance gene detection

Builds proficiency in surveillance and characterization of antimicrobial resistance (AMR) and virulence traits through genomic tools

Provides a strong basis for professionals working in surveillance of bacterial pathogens and antimicrobial resistance

Reviews summary

Microbes: sequenced and analyzed

learners say this course is largely positive and gives a practical introduction to analyzing whole genome sequencing (WGS) for bacteria. Students find the instructors engaging and the assignments to be well designed, especially the final project. The course is particularly well received by those with little to no bioinformatics experience as it begins with the basics and gradually introduces more advanced concepts, covering topics like serotyping of plasmids, subtyping of bacteria and constructing phylogenetic trees. The main takeaway from reviews is that the course gives learners a solid foundation in using bioinformatics tools for whole genome analysis.

Assignments are relevant, challenging, and help learners apply what they've learned.

"The course explicitly consist all tool of bioinformatics to demonstrate resistance and species profile of bacteria."

"I highly recommend this course, even for me a non molecular biologist/medical student, it was very helpful and very enriching."

"The course is really interesting and knowledgeable for me."

The course is accessible to learners with little to no prior knowledge in bioinformatics or WGS.

"I am an undergraduate student and have worked with bacteria and have also conducted antimicrobial assays for bacteria (like MIC)."

"Apart from wet-lab, I also wanted to have dry-lab experience in this field. "Whole-genome sequencing of bacterial genomes - tools and applications" by DTU really helped me a lot in understanding the basics of this field and has also introduced me to their user-friendly web-based bioinformatic tools developed and hosted by Centre of Genomic Epidemiology."

"This is an amazing experience in understanding the nature and function of genome sequencing."

Instructors are knowledgeable, enthusiastic, and make the material easy to understand.

"Very well explained and interesting course."

"Excellent course with easy to understand explanation and illustration from the instructors."

"A really great option to learn how to use web tools for genomic analysis. It is well explained"

"This course is fundamentally to a biotechnologist, as whole genome sequencing is a significant subject and gives us insight into the various tools and techniques available to study and analyze bacterial genomes."

"Thank You Ever So Much, Ms. Pimlapas L, and others, really grateful for this course. Quite engaging, learnt new Bioinformatics tools, and further improved my understanding of Whole Genome Sequencing (WGS). Thank You"

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 Whole genome sequencing of bacterial genomes - tools and applications with these activities:

Create a comprehensive study guide

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Organize course notes, assignments, and materials for efficient revision

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Gather all relevant course materials
Create an outline and structure for the guide
Summarize key concepts and important information

Brush up on genetics basics

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Review basic genetics concepts to solidify foundational understanding before the course.

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Read textbooks or articles on genetics
Take practice quizzes or review tests
Discuss concepts with peers or mentors

Learn about NGS by Watching a Tutorial

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Enhance your understanding of NGS technology by exploring its principles and applications through guided tutorials.

Browse courses on Next-Generation Sequencing

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Identify relevant NGS tutorials
Watch and take notes on the tutorials
Summarize the key concepts of NGS

Ten other activities

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Organize a study group

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Collaboratively review concepts, practice analysis, and prepare for assessments

Browse courses on Whole Genome Sequencing

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Gather a group of classmates
Set regular meeting times
Assign discussion topics or analysis exercises

Join a study group or online forum

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Enhance understanding by engaging with peers through discussions and shared resources.

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Find or create a study group or join an online forum dedicated to WGS
Discuss course concepts, share insights, and ask questions
Collaborate on projects or assignments

Compile a dataset of real-world WGS data

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Gain exposure to and familiarize yourself with datasets you may encounter in the field

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Identify sources of real-world WGS data
Download and organize data from reputable databases
Include metadata and ensure data quality
Document your data sources and methods

Explore bioinformatics tools

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Get familiar with bioinformatics tools to enhance understanding of WGS applications.

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Follow tutorials on using tools like BLAST, ClustalW, or MEGA
Practice using these tools on sample datasets
Attend online workshops or webinars on bioinformatics tools

Attend industry workshop on WGS technologies

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Gain insights from experts, learn about industry trends, and expand your network

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Identify relevant industry events
Attend workshops and network with professionals
Gather materials and take notes for future reference

Practice WGS Analysis

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Repeat the bioinformatic analysis tools and pipelines you learned by applying them to different bacteria genomes

Browse courses on Whole Genome Sequencing

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Choose a bacterial genome assembly from NCBI
Use the BioProject resource from NCBI
Download the assembly FASTA file and analyze it with WGS tools
Optional: Include a control genome and compare results

Create a tutorial for a genomic analysis tool

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Deepen your understanding of an analysis tool and benefit your fellow learners by creating a tutorial

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Choose a genomic analysis tool from the course
Create a step-by-step tutorial
Explain tool usage and interpretation
Share your tutorial online or with classmates

Participate in a research project

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Gain hands-on experience by participating in a research project related to WGS.

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Identify research labs or institutions working on WGS research
Contact the researchers and inquire about volunteer opportunities
Assist with data collection, analysis, or literature review

Participate in a bioinformatics competition

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Test your skills, solve real-world problems, and showcase your abilities in the field

Browse courses on Bioinformatics

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Research and identify relevant competitions
Form a team or participate individually
Apply WGS and bioinformatics knowledge to solve competition tasks

Create a scientific poster or presentation

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Develop communication skills by creating a poster or presentation that showcases WGS applications.

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Choose a topic related to WGS applications
Gather and analyze data to support the topic
Design and create the poster or presentation using visual and textual elements
Present the poster or presentation at a conference or symposium

Career center

Learners who complete Whole genome sequencing of bacterial genomes - tools and applications will develop knowledge and skills that may be useful to these careers:

Computational Biologist

Computational Biologists use computational tools to model biological systems. They develop new algorithms and software to help biologists understand the complex interactions between genes and proteins. Computational Biologists who specialize in genomics use Whole Genome Sequencing to study the genetic basis of disease and to develop new treatments.

See salaries and explore the career path for Computational Biologist

Bioinformatician

Bioinformaticians use computational tools to analyze biological data, such as DNA sequences and protein structures. They develop new algorithms and software to help biologists understand the complex interactions between genes and proteins. Bioinformaticians who specialize in genomics use Whole Genome Sequencing to study the genetic basis of disease and to develop new treatments.

See salaries and explore the career path for Bioinformatician

Research Scientist

Research Scientists conduct research to advance knowledge in their field. They design and conduct experiments, analyze data, and publish their findings in scientific journals. Research Scientists in the field of genomics often use Whole Genome Sequencing to study the genetic basis of disease and to develop new treatments.

See salaries and explore the career path for Research Scientist

Public Health Geneticist

Public Health Geneticists work to improve the health of populations by understanding the genetic basis of disease. They develop and implement programs to prevent and treat genetic diseases, and they counsel families at risk for genetic disorders. Public Health Geneticists need to have a strong understanding of genomics, as this field is essential for understanding the genetic basis of disease and developing new treatments.

See salaries and explore the career path for Public Health Geneticist

Microbiologist

Microbiologists study microorganisms, such as bacteria, viruses, fungi, and parasites. They are interested in how these organisms cause disease, how they can be prevented and treated, and how they can be used to develop new drugs and vaccines. Microbiologists need to have a strong understanding of genomics, as this field is essential for understanding the mechanisms of microbial pathogenesis and developing new antimicrobial therapies.

See salaries and explore the career path for Microbiologist

Systems Biologist

Systems Biologists use a holistic approach to study biological systems. They develop new models and tools to help biologists understand how genes, proteins, and other molecules interact to form complex systems. Systems Biologists who specialize in genomics use Whole Genome Sequencing to study the genetic basis of disease and to develop new treatments.

See salaries and explore the career path for Systems Biologist

Molecular Biologist

Molecular Biologists study the structure and function of DNA, RNA, and proteins. They are interested in how these molecules interact to control cell growth, division, and differentiation. Molecular Biologists often need to use genomic techniques to study the expression of genes and to identify mutations that cause disease.

See salaries and explore the career path for Molecular Biologist

Data Scientist

Data Scientists use statistical and computational methods to analyze large datasets. They develop new algorithms and software to help businesses and organizations make better decisions. Data Scientists who specialize in genomics use Whole Genome Sequencing to study the genetic basis of disease and to develop new treatments.

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Veterinarian

Veterinarians provide medical care to animals. They diagnose and treat diseases, perform surgeries, and prescribe medications. Veterinarians need to have a strong understanding of genomics, as this field is essential for understanding the genetic basis of animal diseases and developing new treatments.

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Software Engineer

Software Engineers design, develop, and maintain software systems. They use their knowledge of computer science to solve problems and create new applications. Software Engineers who specialize in genomics use Whole Genome Sequencing to study the genetic basis of disease and to develop new treatments.

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Physician

Physicians provide medical care to patients. They diagnose and treat diseases, perform surgeries, and prescribe medications. Physicians need to have a strong understanding of genomics, as this field is essential for understanding the genetic basis of disease and developing new treatments.

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Biostatistician

A Biostatistician uses their talents to design experiments, collect data, interpret data, and present findings. This course, Whole Genome Sequencing of Bacterial Genomes, can help those in the field, as this role often deals with large datasets and statistical analysis, as well as the ability to understand and conduct genomic studies.

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Teacher

Teachers educate students in a variety of subjects, including science. Teachers who specialize in genomics need to have a strong understanding of the field, as well as the ability to communicate complex information to students in a clear and engaging way.

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Science Writer

Science Writers communicate complex scientific information to a lay audience. They write articles, books, and other materials that explain scientific discoveries and their implications for society. Science Writers who specialize in genomics need to have a strong understanding of the field, as well as the ability to write clearly and concisely.

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Epidemiologist

Epidemiologists study the distribution and patterns of health-related events and diseases in a population. They design studies and surveys, analyze data, and make recommendations to prevent and control diseases. Epidemiologists often need to understand the underlying mechanisms of disease, which is where knowledge of genomics from this course can be helpful.

See salaries and explore the career path for Epidemiologist