- Course overview
- Search within this course
- Introduction
- Course materials and software
- Metagenomics bioinformatics – course introduction
- Quality control and host decontamination
- The European Nucleotide Archive
- Tools to assemble short reads
- MGnify services
- MGnifyR
- Binning and MAG generation
- ENA metagenomics standards
- MGnify MAG resources
- Strain resolution
- Tools for comparative metagenomics
- Your feedback
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
Course materials and software
MGnify team resources
You will find all of the MGnify team’s practical resources collated together on their Read the Docs site. During the course we will link to the Read The Docs site when there is a specific practical exercise for you to undertake.
MGnify Docker container
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. Please be aware that there is no guarantee the container will work on your personal machine and that the practicals will take longer to run on less powerful machines.
Other software
The software required for the non-EBI trainer’s practicals are generally detailed on the GitHub repositories that accompany their other practical materials. You will need to install this software, and any dependencies, yourself for these practicals to run. If you have difficulties, contacting the trainer in question is the best approach as the EMBL-EBI Training Team will not be able to assist you.
FTP site
The EMBL-EBI Training Team maintain an FTP site of all their course materials. When relevant we will link to the FTP site to provide access to lecture slides, exercise handouts, and other materials.
Either click the link below or copy it into your own browser of FTP client. If prompted, select “Guest” to access the site. You do not need a login.
You can also access the parent folder and all the other materials on the FTP site by clicking on the “…/” at the top of the course page.
Recordings
All of the lecture sessions delivered during the course were recorded and are available from the EMBL-EBI Panopto site. Throughout this course, we will link you to specific recordings within Panopto. You can also access all of the recordings here, or via these playlists for each day of the course: