MGnify Genomes Catalogues

In the presentation we will cover:

  • Recap of MAG generation

  • Overview of MGnify MAG Catalogues

  • Annotations available for catalogues and genomes

  • Metadata available for catalogues and genomes

  • Download files available for catalogues and genomes, via web, FTP, and the API

  • Search mechanisms available against catalogues

MAG Catalogues hands-on exercises

These exercises will use MGnify’s API (“Application programming interface”), showing how your scripts (e.g. Python or R) can talk to the MGnify database.

In partcicular, we’ll be using the API Endpoints (features) associated with viewing and searching MAG Catalogues.

The practical will use a Jupyter Notebook.

Do you have MAGs?

info For the last few exercises, you need some MAGs. If you didn’t get as far as making your own MAGs in the MAG generation exercises, you can copy some we made earlier with this command in a Terminal:

cp -r /media/penelopeprime/Metagenomics-Feb22/Day3/example-mag-bins/* ~/mags

If you DID make your own, copy them to ~/mags.

Opening the Jupyter notebook

action Open a new Terminal. There should be a Terminal application icon in the lefthand menubar.

action Type these commands to enter the repository:

cd ~/symbnet-2022

conda activate mgnify-ebi-2022

info That should have worked, but if you got an error you’ll need to create the environment:

conda create --n mgnify-ebi-2022 python=3.9

conda activate mgnify-ebi-2022

pip install -r requirements.txt

action To open the notebooks, run:

jupyter-lab course.jupyterlab-workspace

Today’s Notebook is “Day 3”.