• Wellcome Connecting Science

Eukaryotic Genome Assembly: How to Use BlobToolKit for Quality Assessment

4.7 (9 reviews)

Gain practical skills in using the BlobToolKit to assess the quality of a eukaryotic genome assembly and improve your research.

1,151 enrolled on this course

A researcher working with Blobtoolkit for quality assessment of a eukaryotic genome assembly on her computer screen.

  • Duration

    3 weeks

  • Weekly study

    3 hours

  • Digital upgrade

    Free
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Discover how genome sequencing is moving beyond humans and model organisms

The BlobToolKit software is an essential tool for the quality assessment of novel genomes. It is being used to support the ambitious EarthBioGenome project to sequence the genomes of all 1.5 million eukaryotic species on the planet, not just humans or model organisms.

On this three-week course, you’ll gain the skills to assess the quality of published novel genomes and detect the presence of multiple organisms within a sample – including parasites, symbionts, and contaminants. This is vital to ensure that newly assembled genomes are high quality.

With this knowledge, you’ll be prepared to use these approaches with your own projects to improve your work.

Take your genomic research further

As you delve into BlobtoolKit, you’ll learn how to select an organism and interpret the blob plot to determine what it shows. Next, you’ll learn how to navigate the BlobToolKit viewer, including filtering and different settings.

With this knowledge, you’ll be able to interpret the visual representations of genomes from samples containing multiple organisms.

Learn how to clean a genome assembly

You’ll learn how to go further with BlobToolKit with techniques such as cleaning a genome assembly and assessing newly generated data.

You’ll also learn how to access genome assemblies from public databases and repositories and use the toolkit to assess their quality.

Develop practical skills in genome sequencing

Throughout the course, you’ll have the opportunity to put what you have learned into practice through different exercises. This includes a peer review course assignment to cement your knowledge.

Guided by the experts at Wellcome Connecting Science, you’ll finish the course with the skills to improve the quality of your genome work with BlobToolKit.

Download video: standard or HD

Skip to 0 minutes and 17 seconds I’m Sujai Kumar, and I’d like to welcome you to this course on eukaryotic genome assembly and how to use BlobToolKit for quality assessment. In this three-week course, you’ll learn about BlobToolKit– a powerful set of tools for analysing genome assemblies. You will learn how to use BlobToolKit to make sense of genome assemblies, which may contain multiple organisms. BlobToolKit is available as a webviewer so you can use it with just browser and internet connection. Once you’ve understood the basic functions of BlobToolKit, you’ll be able to try it for yourself and see if you can analyse and clean up a complex genome assembly. Most of the course will show you how to use BlobToolKit to analyse published genome assembly.

Skip to 1 minute and 1 second Towards the end, there’s an optional section on how to instal the tool in your own space so that you can also use it for your own novel assembly. We really hope you enjoy the course, and we look forward to meeting you.

Syllabus

  • Week 1

    What is BlobToolKit?

    • Welcome to Week 1

      Week 1 educators welcoming you to the week's learning about basic BlobToolKit functions.

    • About BlobToolKit

      Explanation of BlobToolKit and why it is useful for research into genome assemblies, with some real-world case studies.

    • Exploring the BlobToolKit web viewer

      How to use the BlobToolKit web viewer to select organisms, and how to interpret the BTK plots.

    • Week 1 wrap-up

      Check your progress so far after completing the first week of the course.

  • Week 2

    Navigating with the BlobToolKit viewer

    • Get to know the BlobToolKit viewer

      Guides to using the menu options in the BlobToolKit web viewer to filter the data, change the display, and ask questions about genome assemblies.

    • Using BlobToolKit to examine a single genome assembly

      How the BlobToolKit pipeline processes data and how different kinds of data can be displayed

    • Examining multiple genome assemblies using Datasets

      How to use the Datasets table view to compare statistics across several different genome assemblies.

    • Putting your learning into practice

      Put together all the techniques from week 2 to assess and compare different public assemblies in BlobToolKit

  • Week 3

    Going further with BlobToolKit

    • Welcome to Week 3

      Educators of week 3 welcoming you to the week's learning and practicing analysis of your own data

    • Cleaning an example assembly

      How to clean up genome assembly and some advanced tips

    • Try it for yourself

      Explanation of how you should complete the course assignment, an analysis of the assembly of the _C. olitorius_ jute plant.

    • Course assignment

      About your peer review assignment, and how to submit it

    • Completing the main part of the course

      Wrap up and what's next

    • Using BTK on your own de novo assemblies

      BlobToolKit installation

When would you like to start?

  • Date to be announced

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Learning on this course

On every step of the course you can meet other learners, share your ideas and join in with active discussions in the comments.

What will you achieve?

By the end of the course, you‘ll be able to...

  • Use BlobToolKit to assess the quality of genome assemblies
  • Interpret different visual representations of genome assemblies
  • Describe how to set up and interpret a new genome assembly
  • Evaluate existing genome assemblies which have been shared by using the public BlobToolKit server
  • Identify organisms / symbionts / contaminants using GC-coverage plots

Who is the course for?

This course is designed for those working with genome assembly.

You may be a researcher or genome assembler or you could be working on other stages of genome sequencing pipelines wanting to understand the genome assembly assessment process.

Students and early career researchers who want to develop their skills in genome assembly and its analysis will also benefit from this course.

What software or tools do you need?

You will need a computer such as a desktop or laptop with a large screen (not a mobile phone or tablet). The tool runs in an internet browser and no additional software is needed.

Who will you learn with?

Sujai Kumar

Hi - I'm Sujai and I'm an educator for the Future Learn course on BlobToolKit. I work as a Senior Bioinformatician at the Wellcome Sanger Institute and enjoy hiking in my spare time!

Alice Dennis

I work at the University of Namur (Belgium) but I come originally from California. My research group studies adaptive genomics in non-model invertebrates.

Slimane Khayi

I'm a Bioinformatician/Genomist working as a Research Scientist at INRA (Morocco) with a passion for applying computational methods to genomics research.

Abdoallah Sharaf

I'm a senior bioinformatician at SequAna, Uni-kon. Currently, I co-chair the pilot project of the African BioGenome Project (AfricaBP). I'm interested in comparative genomics and genome evolution.

Yves Hermandez TCHIECHOUA

Soil microbiologist, my interest mainly focuses on arbuscular mycorrhizal fungi (AMF) community, function, and diversity using Genomics and Bioinformatics in diverse ecosystems.

Rachel Berkson

Education Manager at Wellcome Connecting Science, UK. Background in cancer genetics then education. Particularly interested in inclusive education.

Who developed the course?

Wellcome Connecting Science

Wellcome Connecting Science develops and delivers open postgraduates courses and conferences focused on biomedicine.

What's included?

Wellcome Connecting Science are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get:

  • Unlimited access to this course
  • Includes any articles, videos, peer reviews and quizzes
  • Tests to validate your learning
  • A PDF Certificate of Achievement to prove your success when you’re eligible

    • Learning on FutureLearn

    Your learning, your rules

    • Courses are split into weeks, activities, and steps to help you keep track of your learning
    • Learn through a mix of bite-sized videos, long- and short-form articles, audio, and practical activities
    • Stay motivated by using the Progress page to keep track of your step completion and assessment scores

    Join a global classroom

    • Experience the power of social learning, and get inspired by an international network of learners
    • Share ideas with your peers and course educators on every step of the course
    • Join the conversation by reading, @ing, liking, bookmarking, and replying to comments from others

    Map your progress

    • As you work through the course, use notifications and the Progress page to guide your learning
    • Whenever you’re ready, mark each step as complete, you’re in control
    • Complete 90% of course steps and all of the assessments to earn your certificate

    Want to know more about learning on FutureLearn? Using FutureLearn

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