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

Traffic lights

Read about what's good

what should give you pause

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

Tools for bacterial genome sequencing analysis

According to learners, this course provides a solid introduction to Whole Genome Sequencing (WGS) for bacterial analysis. Many found the focus on using online tools to be particularly practical and useful for applying WGS in surveillance and resistance detection. While praised for its clear demonstrations and hands-on exercises, some students felt it lacked depth for more advanced users. It is generally seen as a good starting point for those new to the field, though some external tools mentioned may require updates.

Emphasizes using online tools, not scripting.

"The course focuses heavily on using pre-built online tools, less on command line or scripting."

"Good if you just need to use existing platforms, but not for learning to build pipelines."

"It teaches you *how* to use the tools, not *how* they work internally or how to automate."

"Relies mostly on web-based interfaces for analysis."

Provides a solid basis for beginners in the field.

"This course is an excellent starting point for anyone new to bacterial WGS bioinformatics."

"It gave me a clear overview of WGS applications in my field and the tools available."

"I finally understand the basic principles and applications of WGS after taking this course."

"For someone with limited bioinformatics background, this provided a good foundation."

Demonstrates using key online tools effectively.

"The tool demonstrations and exercises were very helpful in understanding how to use them for real data."

"I appreciated the hands-on approach to using the online analysis platforms; it made the concepts concrete."

"Applying the tools to real data cases solidified my understanding and showed their practical application."

"The course provided practical demonstrations of online tools that are relevant for WGS analysis."

Some external resources may need updating.

"Some links to external tools were broken or the tool interface had changed significantly."

"Found that I had to search for the updated versions of some platforms which took extra time."

"A few tools demonstrated seem to have been updated since the course was made, requiring adjustments."

"Keeping external tool demos up-to-date is challenging, but some parts felt a bit old."

May be too basic for experienced users.

"As an experienced bioinformatician, I found it lacked the depth I needed on algorithms or advanced topics."

"Could use more detail on the underlying methods rather than just demonstrating tool usage."

"Good overview, but doesn't go deep into any one tool or method for advanced analysis."

"Better suited for absolute beginners, not intermediate or advanced learners."

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

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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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

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

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.

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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

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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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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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.

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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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