Who is this course for?

This online course ran virtually between 2-6 November 2020. The lecture sessions were recorded and have been made available here along with the practical exercise guides. Unfortunately we cannot provide compute or support to help install the various software packages used during the course, but Docker containers and GitHub repositories should help in setting up your own environment to try out the computational parts of the course.

A full overview of the live course, including the programme, can be found here.

This course will cover the metagenomics data analysis workflow from the point of newly generated sequence data. Participants will explore the use of publicly available resources and tools to manage, share, analyse and interpret metagenomics data. The content will include issues of data quality control and how to submit to public repositories. While sessions will detail marker-gene and whole-genome shotgun (WGS) approaches; the primary focus will be on assembly-based approaches. Discussions will also explore considerations when assembling metagenomic data, the analysis that can be carried out by MGnify on such datasets, and what downstream analysis options and tools are available.

This course is aimed at life scientists who are working in the field of metagenomics and are currently in the early stages of data analysis. Participants should have some prior experience of using bioinformatics in their research.

The practical sessions in the course require a basic understanding of the Unix command line and the R statistics package. Participants might want to work through these free tutorials before attending the course:

• Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix
• Basic R concept tutorials: www.r-tutor.com/r-introduction

What will I achieve?

By the end of the course you will be able to:

• Conduct appropriate quality control and decontamination of metagenomic data and run simple assembly pipelines on short-read data
• Utilise public datasets and resources to identify relevant data for analysis
• Apply appropriate tools in the analysis of metagenomic data
• Submit metagenomics data to online repositories for sharing and future analysis
• Apply relevant knowledge in strain resolution and comparative metagenomic analysis to their own research

What resources do I need?

In order to run the MGnify practicals from the course, you will need to make use of several Docker containers. These software packages contains all the tools and data you need for the MGnify practicals to work. All you need to do is download and run the relevant container on your local machine, meaning you will not need to worry about installing the individual software programmes yourself. The course materials and software page has more information.

DOI: 10.6019/TOL.Metagenomics-t.2019.00001.1

Course contents

How and when to access the course

All our courses are designed with flexibility in mind. You can access them for free at any time, just click on the "Enter Course" button.

It is up to you how you use the course; you can either study the full course or you can focus on sections that are relevant to you. To jump between sections, use the navigation bar on the left or the arrows at the bottom of the page. You can also choose whether to complete the course in one go, or over several visits.

The average time to read through the main body of the course is 3 hours (not including exercises and external links). The time may vary depending on your prior knowledge and how you choose to work through the course.

Sign up to track your learning and more

You can track your progress and keep a record of any completed learning by creating an account. This will give you a 'My learning' page, which will have three main tabs to help keep track of your progress:

Favourite: To add online tutorials to your Favourite tab, you can 'Mark as Favourite' on the front page of online tutorials, allowing you to return and complete them in the future.

In progress: The courses which you have started reading will be added to your 'In progress' tab. Use the 'Mark as complete' button at the end of the course pages to get started.Your ‘In progress’ tab gets updated as you progress through the course and will show you what percentage of the course you have finished and will let you resume the course from where you left on your last visit.

Completed: The courses which you have finished entirely will be added to the 'Completed' tab.

The results you gain from completing quizzes and other interactive content will also be added to your My learning page.

You can register anytime here or click a 'Favourite' or 'Mark as complete' button to start tracking your progress.

You can still access all the online tutorials and interactive content if you do not register, but you will not be able to track your progress.

Making the most of the course

Learning something new takes time and practice. We encourage you to:

• Use the activities and quizzes to help you check your learning, recall and apply key concepts. Look out for these icons 

  Activities

  Quizzes

  Videos

• Revisit sections as and when you need them. Bookmark relevant pages in your browser or use the navigation panel to jump the relevant section.

Getting help and providing feedback

If something isn’t working or if you have a question get in touch by contacting us at trainonline@ebi.ac.uk

Tell us what you thought about the course (both good and bad!) using the “Feedback and help” button found at the top of each page.

Your feedback helps us ensure we are providing training that is relevant and useful for you.

For help and support on EMBL-EBI resources you can contact the helpdesk directly.

Learn more

You can explore other training on offer from EMBL-EBI on our website. We offer online courses, webinars, face-to-face courses and offsite training.